Starting phenix.real_space_refine on Wed Sep 25 09:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/09_2024/6wq2_21868.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/09_2024/6wq2_21868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/09_2024/6wq2_21868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/09_2024/6wq2_21868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/09_2024/6wq2_21868.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/09_2024/6wq2_21868.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 448 5.49 5 S 204 5.16 5 C 34757 2.51 5 N 9337 2.21 5 O 11494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 205 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56240 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 4613 Classifications: {'DNA': 225} Link IDs: {'rna3p': 224} Chain: "2" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 4571 Classifications: {'DNA': 223} Link IDs: {'rna3p': 222} Chain: "A" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "N" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "T" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "a" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "d" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "f" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "g" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "h" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "j" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "k" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "l" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "m" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "n" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "p" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "r" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "t" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 22.70, per 1000 atoms: 0.40 Number of scatterers: 56240 At special positions: 0 Unit cell: (161, 159.6, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 448 15.00 O 11494 8.00 N 9337 7.00 C 34757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 4.5 seconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11322 Finding SS restraints... Secondary structure from input PDB file: 289 helices and 17 sheets defined 77.3% alpha, 2.2% beta 223 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 14.37 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.845A pdb=" N GLY A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 39 through 60 Processing helix chain 'A' and resid 61 through 79 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.539A pdb=" N ILE A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.564A pdb=" N VAL B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 39 through 60 Processing helix chain 'B' and resid 61 through 79 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.941A pdb=" N GLY C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 39 through 60 Processing helix chain 'C' and resid 61 through 79 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.566A pdb=" N VAL D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 39 through 60 Processing helix chain 'D' and resid 61 through 79 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.775A pdb=" N GLY E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 39 through 60 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'E' and resid 81 through 99 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 150 through 166 Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.898A pdb=" N GLY F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 39 through 60 Processing helix chain 'F' and resid 61 through 79 Processing helix chain 'F' and resid 81 through 99 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.865A pdb=" N GLY G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 39 Processing helix chain 'G' and resid 39 through 60 Processing helix chain 'G' and resid 61 through 79 Processing helix chain 'G' and resid 81 through 99 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.503A pdb=" N ILE G 111 " --> pdb=" O PRO G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 166 Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.850A pdb=" N GLY H 29 " --> pdb=" O ILE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 39 through 60 Processing helix chain 'H' and resid 61 through 79 Processing helix chain 'H' and resid 81 through 99 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.865A pdb=" N GLY I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 39 Processing helix chain 'I' and resid 39 through 60 Processing helix chain 'I' and resid 61 through 79 Processing helix chain 'I' and resid 81 through 99 Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 150 through 166 Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.858A pdb=" N GLY J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 39 through 60 Processing helix chain 'J' and resid 61 through 79 Processing helix chain 'J' and resid 81 through 99 Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 150 through 165 removed outlier: 3.646A pdb=" N VAL J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.871A pdb=" N GLY K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 39 Processing helix chain 'K' and resid 39 through 60 Processing helix chain 'K' and resid 61 through 79 Processing helix chain 'K' and resid 81 through 99 Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 150 through 166 Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.792A pdb=" N GLY L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 39 removed outlier: 3.667A pdb=" N ILE L 36 " --> pdb=" O ASN L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 60 Processing helix chain 'L' and resid 61 through 79 Processing helix chain 'L' and resid 81 through 99 Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.804A pdb=" N GLY M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 Processing helix chain 'M' and resid 39 through 60 Processing helix chain 'M' and resid 61 through 79 Processing helix chain 'M' and resid 81 through 99 Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.538A pdb=" N ILE M 111 " --> pdb=" O PRO M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 166 Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.824A pdb=" N GLY N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 39 Processing helix chain 'N' and resid 39 through 60 Processing helix chain 'N' and resid 61 through 79 Processing helix chain 'N' and resid 81 through 99 Processing helix chain 'N' and resid 107 through 120 Processing helix chain 'N' and resid 150 through 165 removed outlier: 3.538A pdb=" N VAL N 165 " --> pdb=" O LEU N 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.847A pdb=" N GLY P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 39 Processing helix chain 'P' and resid 39 through 60 Processing helix chain 'P' and resid 61 through 79 Processing helix chain 'P' and resid 81 through 99 Processing helix chain 'P' and resid 107 through 120 Processing helix chain 'P' and resid 150 through 165 Processing helix chain 'R' and resid 9 through 29 removed outlier: 3.810A pdb=" N GLY R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 39 Processing helix chain 'R' and resid 39 through 60 Processing helix chain 'R' and resid 61 through 79 Processing helix chain 'R' and resid 81 through 99 Processing helix chain 'R' and resid 107 through 120 Processing helix chain 'R' and resid 150 through 165 removed outlier: 3.626A pdb=" N VAL R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 29 removed outlier: 4.038A pdb=" N GLY T 29 " --> pdb=" O ILE T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 39 removed outlier: 3.608A pdb=" N ASN T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 60 Processing helix chain 'T' and resid 61 through 79 Processing helix chain 'T' and resid 81 through 99 Processing helix chain 'T' and resid 107 through 120 Processing helix chain 'T' and resid 150 through 165 removed outlier: 3.568A pdb=" N VAL T 165 " --> pdb=" O LEU T 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 15 through 33 removed outlier: 4.636A pdb=" N ASN a 30 " --> pdb=" O GLY a 26 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 72 removed outlier: 4.485A pdb=" N GLU a 54 " --> pdb=" O ASP a 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS a 58 " --> pdb=" O GLU a 54 " (cutoff:3.500A) Proline residue: a 65 - end of helix Processing helix chain 'a' and resid 76 through 90 removed outlier: 3.522A pdb=" N VAL a 90 " --> pdb=" O ALA a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 108 removed outlier: 3.682A pdb=" N LEU a 101 " --> pdb=" O THR a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 130 removed outlier: 4.117A pdb=" N GLU a 128 " --> pdb=" O ASN a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 138 removed outlier: 3.552A pdb=" N ALA a 134 " --> pdb=" O VAL a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 158 Processing helix chain 'a' and resid 162 through 168 removed outlier: 4.173A pdb=" N ALA a 166 " --> pdb=" O PRO a 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL a 168 " --> pdb=" O SER a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 174 removed outlier: 4.234A pdb=" N VAL a 174 " --> pdb=" O MET a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 202 removed outlier: 3.601A pdb=" N LYS a 195 " --> pdb=" O GLU a 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 33 removed outlier: 4.569A pdb=" N ASN b 30 " --> pdb=" O GLY b 26 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR b 31 " --> pdb=" O ILE b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 72 removed outlier: 4.612A pdb=" N GLU b 54 " --> pdb=" O ASP b 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS b 58 " --> pdb=" O GLU b 54 " (cutoff:3.500A) Proline residue: b 65 - end of helix Processing helix chain 'b' and resid 76 through 90 removed outlier: 3.554A pdb=" N VAL b 90 " --> pdb=" O ALA b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 97 through 108 removed outlier: 3.681A pdb=" N LEU b 101 " --> pdb=" O THR b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 130 removed outlier: 4.051A pdb=" N GLU b 128 " --> pdb=" O ASN b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 138 Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 163 through 168 removed outlier: 3.650A pdb=" N VAL b 168 " --> pdb=" O SER b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 174 removed outlier: 4.132A pdb=" N VAL b 174 " --> pdb=" O MET b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 202 removed outlier: 4.157A pdb=" N SER b 192 " --> pdb=" O SER b 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS b 195 " --> pdb=" O GLU b 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 33 removed outlier: 4.391A pdb=" N ASN c 30 " --> pdb=" O GLY c 26 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR c 31 " --> pdb=" O ILE c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 72 removed outlier: 4.554A pdb=" N GLU c 54 " --> pdb=" O ASP c 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS c 58 " --> pdb=" O GLU c 54 " (cutoff:3.500A) Proline residue: c 65 - end of helix Processing helix chain 'c' and resid 76 through 90 removed outlier: 3.507A pdb=" N VAL c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 108 removed outlier: 3.690A pdb=" N LEU c 101 " --> pdb=" O THR c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 130 removed outlier: 3.920A pdb=" N GLU c 128 " --> pdb=" O ASN c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 138 Processing helix chain 'c' and resid 146 through 158 Processing helix chain 'c' and resid 163 through 168 removed outlier: 3.801A pdb=" N VAL c 168 " --> pdb=" O SER c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 174 removed outlier: 3.951A pdb=" N VAL c 174 " --> pdb=" O MET c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 189 through 202 removed outlier: 3.678A pdb=" N LYS c 195 " --> pdb=" O GLU c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 33 removed outlier: 4.665A pdb=" N ASN d 30 " --> pdb=" O GLY d 26 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR d 31 " --> pdb=" O ILE d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 72 removed outlier: 4.551A pdb=" N GLU d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Proline residue: d 65 - end of helix Processing helix chain 'd' and resid 76 through 90 removed outlier: 3.629A pdb=" N VAL d 90 " --> pdb=" O ALA d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 108 removed outlier: 3.805A pdb=" N LEU d 101 " --> pdb=" O THR d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 130 removed outlier: 4.077A pdb=" N GLU d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 138 Processing helix chain 'd' and resid 146 through 158 Processing helix chain 'd' and resid 163 through 168 removed outlier: 3.772A pdb=" N VAL d 168 " --> pdb=" O SER d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 174 removed outlier: 4.334A pdb=" N VAL d 174 " --> pdb=" O MET d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 removed outlier: 4.113A pdb=" N SER d 192 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 33 removed outlier: 4.659A pdb=" N ASN e 30 " --> pdb=" O GLY e 26 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR e 31 " --> pdb=" O ILE e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 72 removed outlier: 4.512A pdb=" N GLU e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS e 58 " --> pdb=" O GLU e 54 " (cutoff:3.500A) Proline residue: e 65 - end of helix Processing helix chain 'e' and resid 76 through 90 Processing helix chain 'e' and resid 97 through 108 removed outlier: 3.683A pdb=" N LEU e 101 " --> pdb=" O THR e 97 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 130 removed outlier: 4.088A pdb=" N GLU e 128 " --> pdb=" O ASN e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 138 removed outlier: 3.626A pdb=" N ALA e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 158 Processing helix chain 'e' and resid 163 through 168 removed outlier: 3.698A pdb=" N VAL e 168 " --> pdb=" O SER e 164 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 174 removed outlier: 4.282A pdb=" N VAL e 174 " --> pdb=" O MET e 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 202 removed outlier: 3.580A pdb=" N LYS e 195 " --> pdb=" O GLU e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 33 removed outlier: 4.424A pdb=" N ASN f 30 " --> pdb=" O GLY f 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR f 31 " --> pdb=" O ILE f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 72 removed outlier: 4.549A pdb=" N GLU f 54 " --> pdb=" O ASP f 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS f 58 " --> pdb=" O GLU f 54 " (cutoff:3.500A) Proline residue: f 65 - end of helix Processing helix chain 'f' and resid 76 through 90 Processing helix chain 'f' and resid 97 through 108 removed outlier: 3.672A pdb=" N LEU f 101 " --> pdb=" O THR f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 130 removed outlier: 4.053A pdb=" N GLU f 128 " --> pdb=" O ASN f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 138 Processing helix chain 'f' and resid 146 through 158 Processing helix chain 'f' and resid 163 through 168 Processing helix chain 'f' and resid 168 through 174 removed outlier: 4.231A pdb=" N VAL f 174 " --> pdb=" O MET f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 189 through 202 removed outlier: 3.627A pdb=" N LYS f 195 " --> pdb=" O GLU f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 33 removed outlier: 4.438A pdb=" N ASN g 30 " --> pdb=" O GLY g 26 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 72 removed outlier: 4.475A pdb=" N GLU g 54 " --> pdb=" O ASP g 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS g 58 " --> pdb=" O GLU g 54 " (cutoff:3.500A) Proline residue: g 65 - end of helix Processing helix chain 'g' and resid 76 through 90 Processing helix chain 'g' and resid 97 through 108 removed outlier: 3.723A pdb=" N LEU g 101 " --> pdb=" O THR g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 130 removed outlier: 4.100A pdb=" N GLU g 128 " --> pdb=" O ASN g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 138 Processing helix chain 'g' and resid 146 through 158 Processing helix chain 'g' and resid 163 through 168 removed outlier: 3.647A pdb=" N VAL g 168 " --> pdb=" O SER g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 174 removed outlier: 4.182A pdb=" N VAL g 174 " --> pdb=" O MET g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 189 through 202 removed outlier: 3.666A pdb=" N LYS g 195 " --> pdb=" O GLU g 191 " (cutoff:3.500A) Processing helix chain 'h' and resid 15 through 33 removed outlier: 4.485A pdb=" N ASN h 30 " --> pdb=" O GLY h 26 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR h 31 " --> pdb=" O ILE h 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 72 removed outlier: 4.461A pdb=" N GLU h 54 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS h 58 " --> pdb=" O GLU h 54 " (cutoff:3.500A) Proline residue: h 65 - end of helix Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.612A pdb=" N VAL h 90 " --> pdb=" O ALA h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 108 removed outlier: 3.757A pdb=" N LEU h 101 " --> pdb=" O THR h 97 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 130 removed outlier: 4.039A pdb=" N GLU h 128 " --> pdb=" O ASN h 124 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 138 Processing helix chain 'h' and resid 146 through 158 Processing helix chain 'h' and resid 163 through 168 removed outlier: 3.706A pdb=" N VAL h 168 " --> pdb=" O SER h 164 " (cutoff:3.500A) Processing helix chain 'h' and resid 168 through 174 removed outlier: 4.042A pdb=" N VAL h 174 " --> pdb=" O MET h 170 " (cutoff:3.500A) Processing helix chain 'h' and resid 188 through 202 removed outlier: 4.226A pdb=" N SER h 192 " --> pdb=" O SER h 188 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS h 195 " --> pdb=" O GLU h 191 " (cutoff:3.500A) Processing helix chain 'i' and resid 15 through 33 removed outlier: 4.303A pdb=" N ASN i 30 " --> pdb=" O GLY i 26 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR i 31 " --> pdb=" O ILE i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 72 removed outlier: 4.481A pdb=" N GLU i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS i 58 " --> pdb=" O GLU i 54 " (cutoff:3.500A) Proline residue: i 65 - end of helix Processing helix chain 'i' and resid 76 through 90 removed outlier: 3.578A pdb=" N VAL i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 108 removed outlier: 3.771A pdb=" N LEU i 101 " --> pdb=" O THR i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 130 removed outlier: 4.068A pdb=" N GLU i 128 " --> pdb=" O ASN i 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 130 through 138 removed outlier: 3.526A pdb=" N ALA i 134 " --> pdb=" O VAL i 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 158 Processing helix chain 'i' and resid 162 through 168 removed outlier: 4.167A pdb=" N ALA i 166 " --> pdb=" O PRO i 162 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL i 168 " --> pdb=" O SER i 164 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 174 removed outlier: 4.048A pdb=" N VAL i 174 " --> pdb=" O MET i 170 " (cutoff:3.500A) Processing helix chain 'i' and resid 189 through 202 removed outlier: 3.695A pdb=" N LYS i 195 " --> pdb=" O GLU i 191 " (cutoff:3.500A) Processing helix chain 'j' and resid 15 through 33 removed outlier: 4.449A pdb=" N ASN j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR j 31 " --> pdb=" O ILE j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 72 removed outlier: 4.478A pdb=" N GLU j 54 " --> pdb=" O ASP j 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS j 58 " --> pdb=" O GLU j 54 " (cutoff:3.500A) Proline residue: j 65 - end of helix Processing helix chain 'j' and resid 76 through 90 Processing helix chain 'j' and resid 97 through 108 removed outlier: 3.786A pdb=" N LEU j 101 " --> pdb=" O THR j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 130 removed outlier: 4.076A pdb=" N GLU j 128 " --> pdb=" O ASN j 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 138 Processing helix chain 'j' and resid 146 through 158 Processing helix chain 'j' and resid 162 through 168 removed outlier: 4.136A pdb=" N ALA j 166 " --> pdb=" O PRO j 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL j 168 " --> pdb=" O SER j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 174 removed outlier: 4.145A pdb=" N VAL j 174 " --> pdb=" O MET j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 189 through 202 removed outlier: 3.708A pdb=" N LYS j 195 " --> pdb=" O GLU j 191 " (cutoff:3.500A) Processing helix chain 'k' and resid 15 through 33 removed outlier: 4.375A pdb=" N ASN k 30 " --> pdb=" O GLY k 26 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR k 31 " --> pdb=" O ILE k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 72 removed outlier: 4.499A pdb=" N GLU k 54 " --> pdb=" O ASP k 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Proline residue: k 65 - end of helix Processing helix chain 'k' and resid 76 through 90 Processing helix chain 'k' and resid 97 through 108 removed outlier: 3.622A pdb=" N LEU k 101 " --> pdb=" O THR k 97 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 130 removed outlier: 4.124A pdb=" N GLU k 128 " --> pdb=" O ASN k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 138 Processing helix chain 'k' and resid 146 through 158 Processing helix chain 'k' and resid 162 through 168 removed outlier: 4.150A pdb=" N ALA k 166 " --> pdb=" O PRO k 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL k 168 " --> pdb=" O SER k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 168 through 174 removed outlier: 3.981A pdb=" N VAL k 174 " --> pdb=" O MET k 170 " (cutoff:3.500A) Processing helix chain 'k' and resid 189 through 202 removed outlier: 3.681A pdb=" N LYS k 195 " --> pdb=" O GLU k 191 " (cutoff:3.500A) Processing helix chain 'l' and resid 15 through 33 removed outlier: 4.631A pdb=" N ASN l 30 " --> pdb=" O GLY l 26 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR l 31 " --> pdb=" O ILE l 27 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 72 removed outlier: 4.464A pdb=" N GLU l 54 " --> pdb=" O ASP l 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS l 58 " --> pdb=" O GLU l 54 " (cutoff:3.500A) Proline residue: l 65 - end of helix Processing helix chain 'l' and resid 76 through 90 removed outlier: 3.533A pdb=" N VAL l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 108 removed outlier: 3.751A pdb=" N LEU l 101 " --> pdb=" O THR l 97 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 130 removed outlier: 4.000A pdb=" N GLU l 128 " --> pdb=" O ASN l 124 " (cutoff:3.500A) Processing helix chain 'l' and resid 130 through 138 Processing helix chain 'l' and resid 146 through 158 Processing helix chain 'l' and resid 162 through 168 removed outlier: 4.231A pdb=" N ALA l 166 " --> pdb=" O PRO l 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL l 168 " --> pdb=" O SER l 164 " (cutoff:3.500A) Processing helix chain 'l' and resid 168 through 174 removed outlier: 4.184A pdb=" N VAL l 174 " --> pdb=" O MET l 170 " (cutoff:3.500A) Processing helix chain 'l' and resid 188 through 202 removed outlier: 4.285A pdb=" N SER l 192 " --> pdb=" O SER l 188 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS l 195 " --> pdb=" O GLU l 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 15 through 33 removed outlier: 4.484A pdb=" N ASN m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR m 31 " --> pdb=" O ILE m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 72 removed outlier: 4.302A pdb=" N GLU m 54 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS m 58 " --> pdb=" O GLU m 54 " (cutoff:3.500A) Proline residue: m 65 - end of helix Processing helix chain 'm' and resid 76 through 90 removed outlier: 3.529A pdb=" N VAL m 90 " --> pdb=" O ALA m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 108 removed outlier: 3.790A pdb=" N LEU m 101 " --> pdb=" O THR m 97 " (cutoff:3.500A) Processing helix chain 'm' and resid 111 through 130 removed outlier: 4.117A pdb=" N GLU m 128 " --> pdb=" O ASN m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 138 Processing helix chain 'm' and resid 146 through 158 Processing helix chain 'm' and resid 163 through 168 removed outlier: 3.612A pdb=" N VAL m 168 " --> pdb=" O SER m 164 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 174 removed outlier: 4.056A pdb=" N VAL m 174 " --> pdb=" O MET m 170 " (cutoff:3.500A) Processing helix chain 'm' and resid 189 through 202 Processing helix chain 'n' and resid 15 through 33 removed outlier: 4.605A pdb=" N ASN n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR n 31 " --> pdb=" O ILE n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 72 removed outlier: 4.490A pdb=" N GLU n 54 " --> pdb=" O ASP n 50 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS n 58 " --> pdb=" O GLU n 54 " (cutoff:3.500A) Proline residue: n 65 - end of helix Processing helix chain 'n' and resid 76 through 90 Processing helix chain 'n' and resid 97 through 108 removed outlier: 3.693A pdb=" N LEU n 101 " --> pdb=" O THR n 97 " (cutoff:3.500A) Processing helix chain 'n' and resid 111 through 130 removed outlier: 4.095A pdb=" N GLU n 128 " --> pdb=" O ASN n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 130 through 138 Processing helix chain 'n' and resid 146 through 158 Processing helix chain 'n' and resid 163 through 168 removed outlier: 3.594A pdb=" N VAL n 168 " --> pdb=" O SER n 164 " (cutoff:3.500A) Processing helix chain 'n' and resid 168 through 174 removed outlier: 4.203A pdb=" N VAL n 174 " --> pdb=" O MET n 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 188 through 202 removed outlier: 4.229A pdb=" N SER n 192 " --> pdb=" O SER n 188 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS n 195 " --> pdb=" O GLU n 191 " (cutoff:3.500A) Processing helix chain 'p' and resid 15 through 33 removed outlier: 4.548A pdb=" N ASN p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR p 31 " --> pdb=" O ILE p 27 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 72 removed outlier: 4.492A pdb=" N GLU p 54 " --> pdb=" O ASP p 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) Proline residue: p 65 - end of helix Processing helix chain 'p' and resid 76 through 89 Processing helix chain 'p' and resid 97 through 108 removed outlier: 3.675A pdb=" N LEU p 101 " --> pdb=" O THR p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 111 through 130 removed outlier: 3.967A pdb=" N GLU p 128 " --> pdb=" O ASN p 124 " (cutoff:3.500A) Processing helix chain 'p' and resid 130 through 138 removed outlier: 3.546A pdb=" N ALA p 134 " --> pdb=" O VAL p 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 146 through 158 Processing helix chain 'p' and resid 163 through 168 removed outlier: 3.852A pdb=" N VAL p 168 " --> pdb=" O SER p 164 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 174 removed outlier: 4.041A pdb=" N VAL p 174 " --> pdb=" O MET p 170 " (cutoff:3.500A) Processing helix chain 'p' and resid 188 through 202 removed outlier: 4.153A pdb=" N SER p 192 " --> pdb=" O SER p 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS p 195 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 33 removed outlier: 4.497A pdb=" N ASN r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR r 31 " --> pdb=" O ILE r 27 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 72 removed outlier: 4.526A pdb=" N GLU r 54 " --> pdb=" O ASP r 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS r 58 " --> pdb=" O GLU r 54 " (cutoff:3.500A) Proline residue: r 65 - end of helix Processing helix chain 'r' and resid 76 through 90 Processing helix chain 'r' and resid 97 through 108 removed outlier: 3.598A pdb=" N LEU r 101 " --> pdb=" O THR r 97 " (cutoff:3.500A) Processing helix chain 'r' and resid 111 through 130 removed outlier: 4.098A pdb=" N GLU r 128 " --> pdb=" O ASN r 124 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 138 Processing helix chain 'r' and resid 146 through 158 Processing helix chain 'r' and resid 163 through 168 removed outlier: 3.826A pdb=" N VAL r 168 " --> pdb=" O SER r 164 " (cutoff:3.500A) Processing helix chain 'r' and resid 168 through 174 removed outlier: 4.275A pdb=" N VAL r 174 " --> pdb=" O MET r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 189 through 202 removed outlier: 3.720A pdb=" N LYS r 195 " --> pdb=" O GLU r 191 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 33 removed outlier: 4.387A pdb=" N ASN t 30 " --> pdb=" O GLY t 26 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR t 31 " --> pdb=" O ILE t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 33 through 72 removed outlier: 4.717A pdb=" N GLU t 54 " --> pdb=" O ASP t 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS t 58 " --> pdb=" O GLU t 54 " (cutoff:3.500A) Proline residue: t 65 - end of helix Processing helix chain 't' and resid 76 through 90 Processing helix chain 't' and resid 97 through 108 removed outlier: 3.728A pdb=" N LEU t 101 " --> pdb=" O THR t 97 " (cutoff:3.500A) Processing helix chain 't' and resid 111 through 130 removed outlier: 4.089A pdb=" N GLU t 128 " --> pdb=" O ASN t 124 " (cutoff:3.500A) Processing helix chain 't' and resid 130 through 138 Processing helix chain 't' and resid 146 through 158 Processing helix chain 't' and resid 163 through 168 removed outlier: 3.686A pdb=" N VAL t 168 " --> pdb=" O SER t 164 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 174 removed outlier: 4.173A pdb=" N VAL t 174 " --> pdb=" O MET t 170 " (cutoff:3.500A) Processing helix chain 't' and resid 188 through 202 removed outlier: 4.285A pdb=" N SER t 192 " --> pdb=" O SER t 188 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS t 195 " --> pdb=" O GLU t 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 139 Processing sheet with id=AA2, first strand: chain 'B' and resid 135 through 139 Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 139 Processing sheet with id=AA4, first strand: chain 'D' and resid 135 through 139 Processing sheet with id=AA5, first strand: chain 'E' and resid 135 through 139 Processing sheet with id=AA6, first strand: chain 'F' and resid 135 through 139 Processing sheet with id=AA7, first strand: chain 'G' and resid 135 through 139 Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AA9, first strand: chain 'I' and resid 135 through 139 Processing sheet with id=AB1, first strand: chain 'J' and resid 135 through 139 Processing sheet with id=AB2, first strand: chain 'K' and resid 135 through 139 Processing sheet with id=AB3, first strand: chain 'L' and resid 135 through 139 Processing sheet with id=AB4, first strand: chain 'M' and resid 135 through 139 Processing sheet with id=AB5, first strand: chain 'N' and resid 135 through 139 Processing sheet with id=AB6, first strand: chain 'P' and resid 135 through 139 Processing sheet with id=AB7, first strand: chain 'R' and resid 135 through 139 Processing sheet with id=AB8, first strand: chain 'T' and resid 135 through 139 3335 hydrogen bonds defined for protein. 10005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 446 hydrogen bonds 892 hydrogen bond angles 0 basepair planarities 223 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 17.83 Time building geometry restraints manager: 12.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10943 1.33 - 1.45: 15731 1.45 - 1.57: 30351 1.57 - 1.69: 894 1.69 - 1.81: 408 Bond restraints: 58327 Sorted by residual: bond pdb=" C SER p 157 " pdb=" N MET p 158 " ideal model delta sigma weight residual 1.327 1.276 0.051 2.86e-02 1.22e+03 3.13e+00 bond pdb=" C THR j 178 " pdb=" N PRO j 179 " ideal model delta sigma weight residual 1.334 1.319 0.014 8.40e-03 1.42e+04 2.87e+00 bond pdb=" C THR p 178 " pdb=" N PRO p 179 " ideal model delta sigma weight residual 1.334 1.320 0.014 8.40e-03 1.42e+04 2.64e+00 bond pdb=" C THR d 178 " pdb=" N PRO d 179 " ideal model delta sigma weight residual 1.334 1.320 0.014 8.40e-03 1.42e+04 2.63e+00 bond pdb=" C THR t 178 " pdb=" N PRO t 179 " ideal model delta sigma weight residual 1.334 1.320 0.013 8.40e-03 1.42e+04 2.57e+00 ... (remaining 58322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 79553 2.26 - 4.53: 1430 4.53 - 6.79: 130 6.79 - 9.06: 11 9.06 - 11.32: 1 Bond angle restraints: 81125 Sorted by residual: angle pdb=" C SER b 157 " pdb=" N MET b 158 " pdb=" CA MET b 158 " ideal model delta sigma weight residual 122.31 110.99 11.32 2.34e+00 1.83e-01 2.34e+01 angle pdb=" N PRO p 179 " pdb=" CA PRO p 179 " pdb=" C PRO p 179 " ideal model delta sigma weight residual 114.68 110.43 4.25 1.04e+00 9.25e-01 1.67e+01 angle pdb=" N PRO g 179 " pdb=" CA PRO g 179 " pdb=" C PRO g 179 " ideal model delta sigma weight residual 114.68 110.47 4.21 1.04e+00 9.25e-01 1.64e+01 angle pdb=" N PRO d 179 " pdb=" CA PRO d 179 " pdb=" C PRO d 179 " ideal model delta sigma weight residual 114.68 110.60 4.08 1.04e+00 9.25e-01 1.54e+01 angle pdb=" N PRO f 179 " pdb=" CA PRO f 179 " pdb=" C PRO f 179 " ideal model delta sigma weight residual 114.68 110.70 3.98 1.04e+00 9.25e-01 1.46e+01 ... (remaining 81120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 29122 17.87 - 35.75: 3499 35.75 - 53.62: 1115 53.62 - 71.50: 254 71.50 - 89.37: 25 Dihedral angle restraints: 34015 sinusoidal: 16301 harmonic: 17714 Sorted by residual: dihedral pdb=" CA ALA j 73 " pdb=" C ALA j 73 " pdb=" N GLY j 74 " pdb=" CA GLY j 74 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA m 73 " pdb=" C ALA m 73 " pdb=" N GLY m 74 " pdb=" CA GLY m 74 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ALA l 73 " pdb=" C ALA l 73 " pdb=" N GLY l 74 " pdb=" CA GLY l 74 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 34012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 6937 0.042 - 0.084: 1942 0.084 - 0.126: 449 0.126 - 0.168: 11 0.168 - 0.211: 1 Chirality restraints: 9340 Sorted by residual: chirality pdb=" P DA 2 403 " pdb=" OP1 DA 2 403 " pdb=" OP2 DA 2 403 " pdb=" O5' DA 2 403 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' DT 2 406 " pdb=" C4' DT 2 406 " pdb=" O3' DT 2 406 " pdb=" C2' DT 2 406 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" P DT 2 492 " pdb=" OP1 DT 2 492 " pdb=" OP2 DT 2 492 " pdb=" O5' DT 2 492 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 9337 not shown) Planarity restraints: 8642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT 1 150 " 0.027 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" N1 DT 1 150 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DT 1 150 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT 1 150 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT 1 150 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT 1 150 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT 1 150 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT 1 150 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT 1 150 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT 1 150 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 2 487 " 0.030 2.00e-02 2.50e+03 1.52e-02 6.34e+00 pdb=" N9 DA 2 487 " -0.036 2.00e-02 2.50e+03 pdb=" C8 DA 2 487 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA 2 487 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA 2 487 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA 2 487 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA 2 487 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA 2 487 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA 2 487 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA 2 487 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA 2 487 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL n 53 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C VAL n 53 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL n 53 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU n 54 " -0.014 2.00e-02 2.50e+03 ... (remaining 8639 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 999 2.61 - 3.19: 57884 3.19 - 3.76: 102310 3.76 - 4.33: 131727 4.33 - 4.90: 201943 Nonbonded interactions: 494863 Sorted by model distance: nonbonded pdb=" OP1 DA 2 467 " pdb=" OG SER I 12 " model vdw 2.043 3.040 nonbonded pdb=" OP1 DA 2 299 " pdb=" OG SER T 12 " model vdw 2.081 3.040 nonbonded pdb=" OP1 DA 2 383 " pdb=" OG SER F 12 " model vdw 2.087 3.040 nonbonded pdb=" OP1 DA 2 371 " pdb=" OG SER H 12 " model vdw 2.088 3.040 nonbonded pdb=" NE2 HIS H 65 " pdb=" O PHE m 187 " model vdw 2.092 3.120 ... (remaining 494858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and resid 8 through 230) selection = chain '2' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.480 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 98.260 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 58327 Z= 0.315 Angle : 0.709 11.320 81125 Z= 0.420 Chirality : 0.039 0.211 9340 Planarity : 0.005 0.040 8642 Dihedral : 16.892 89.374 22693 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.09), residues: 5950 helix: -1.34 (0.07), residues: 4233 sheet: -1.36 (0.35), residues: 170 loop : -3.08 (0.14), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 117 HIS 0.008 0.001 HIS H 65 PHE 0.023 0.002 PHE b 77 TYR 0.021 0.002 TYR m 45 ARG 0.010 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1736 time to evaluate : 4.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9118 (tpp) cc_final: 0.8817 (mpp) REVERT: A 51 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 52 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8565 (mm-40) REVERT: A 74 ILE cc_start: 0.9790 (mm) cc_final: 0.9375 (mm) REVERT: A 134 PHE cc_start: 0.8898 (m-80) cc_final: 0.8490 (m-10) REVERT: A 144 LYS cc_start: 0.9382 (mttp) cc_final: 0.9100 (mtpp) REVERT: A 157 ILE cc_start: 0.9785 (pt) cc_final: 0.9578 (pt) REVERT: A 158 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 162 PHE cc_start: 0.9568 (m-80) cc_final: 0.9096 (m-80) REVERT: B 43 MET cc_start: 0.9140 (tpp) cc_final: 0.8904 (mpp) REVERT: B 51 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8547 (tm-30) REVERT: B 99 TYR cc_start: 0.8998 (t80) cc_final: 0.8759 (t80) REVERT: B 158 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8627 (mt-10) REVERT: C 27 THR cc_start: 0.9166 (m) cc_final: 0.8910 (p) REVERT: C 39 ASN cc_start: 0.9182 (t0) cc_final: 0.8670 (t0) REVERT: C 51 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8281 (tm-30) REVERT: C 52 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8948 (mm-40) REVERT: C 99 TYR cc_start: 0.9228 (t80) cc_final: 0.8691 (t80) REVERT: C 134 PHE cc_start: 0.8227 (m-80) cc_final: 0.7732 (m-10) REVERT: C 142 ASP cc_start: 0.8833 (p0) cc_final: 0.8574 (p0) REVERT: C 157 ILE cc_start: 0.9808 (pt) cc_final: 0.9297 (pt) REVERT: C 158 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8577 (mt-10) REVERT: C 162 PHE cc_start: 0.9655 (m-80) cc_final: 0.9196 (m-80) REVERT: D 20 ARG cc_start: 0.9073 (mmm160) cc_final: 0.8618 (mmt180) REVERT: D 21 ILE cc_start: 0.9379 (mt) cc_final: 0.9078 (mt) REVERT: D 39 ASN cc_start: 0.9214 (t0) cc_final: 0.8774 (t0) REVERT: D 46 ILE cc_start: 0.9844 (mt) cc_final: 0.9605 (tt) REVERT: D 51 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8726 (tm-30) REVERT: D 134 PHE cc_start: 0.8730 (m-80) cc_final: 0.8059 (m-10) REVERT: D 142 ASP cc_start: 0.9010 (p0) cc_final: 0.8621 (p0) REVERT: D 158 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8528 (mt-10) REVERT: D 162 PHE cc_start: 0.9588 (m-80) cc_final: 0.9365 (m-80) REVERT: E 17 TYR cc_start: 0.9074 (t80) cc_final: 0.8781 (t80) REVERT: E 21 ILE cc_start: 0.9219 (mt) cc_final: 0.8926 (mt) REVERT: E 39 ASN cc_start: 0.9159 (t0) cc_final: 0.8313 (t0) REVERT: E 51 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8708 (tm-30) REVERT: E 52 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8928 (mm-40) REVERT: E 134 PHE cc_start: 0.8170 (m-80) cc_final: 0.7888 (m-10) REVERT: F 17 TYR cc_start: 0.9122 (t80) cc_final: 0.8922 (t80) REVERT: F 21 ILE cc_start: 0.9367 (mt) cc_final: 0.8976 (mt) REVERT: F 27 THR cc_start: 0.9130 (m) cc_final: 0.8925 (m) REVERT: F 51 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 52 GLN cc_start: 0.9394 (mm-40) cc_final: 0.8811 (mm-40) REVERT: F 53 GLU cc_start: 0.8707 (tt0) cc_final: 0.8446 (tp30) REVERT: F 55 TYR cc_start: 0.9135 (t80) cc_final: 0.8887 (t80) REVERT: F 120 MET cc_start: 0.8339 (ppp) cc_final: 0.7976 (ppp) REVERT: F 134 PHE cc_start: 0.8684 (m-80) cc_final: 0.8150 (m-10) REVERT: F 157 ILE cc_start: 0.9791 (pt) cc_final: 0.9457 (pt) REVERT: F 162 PHE cc_start: 0.9489 (m-80) cc_final: 0.9129 (m-80) REVERT: G 27 THR cc_start: 0.9043 (m) cc_final: 0.8703 (p) REVERT: G 51 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8999 (tm-30) REVERT: G 94 LYS cc_start: 0.9523 (ttpt) cc_final: 0.8911 (tppt) REVERT: G 134 PHE cc_start: 0.8644 (m-80) cc_final: 0.8238 (m-10) REVERT: H 20 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8906 (mmt180) REVERT: H 43 MET cc_start: 0.9369 (tpp) cc_final: 0.8899 (mpp) REVERT: H 51 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8892 (tm-30) REVERT: H 52 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9110 (mm-40) REVERT: H 99 TYR cc_start: 0.9270 (t80) cc_final: 0.9063 (t80) REVERT: H 134 PHE cc_start: 0.8465 (m-80) cc_final: 0.8249 (m-80) REVERT: H 158 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8799 (mt-10) REVERT: I 21 ILE cc_start: 0.9217 (mt) cc_final: 0.8865 (mt) REVERT: I 51 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8592 (tm-30) REVERT: I 52 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8826 (mm-40) REVERT: I 89 MET cc_start: 0.9653 (mtt) cc_final: 0.9127 (mtt) REVERT: I 94 LYS cc_start: 0.9559 (ttpt) cc_final: 0.9161 (tptt) REVERT: I 134 PHE cc_start: 0.8645 (m-80) cc_final: 0.8031 (m-80) REVERT: I 157 ILE cc_start: 0.9781 (pt) cc_final: 0.9545 (pt) REVERT: I 158 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8958 (mt-10) REVERT: I 162 PHE cc_start: 0.9449 (m-80) cc_final: 0.9100 (m-80) REVERT: J 21 ILE cc_start: 0.9021 (mt) cc_final: 0.8679 (mt) REVERT: J 53 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8837 (mt-10) REVERT: J 74 ILE cc_start: 0.9682 (mm) cc_final: 0.9223 (mm) REVERT: J 89 MET cc_start: 0.9597 (mtt) cc_final: 0.9385 (mtp) REVERT: J 99 TYR cc_start: 0.9054 (t80) cc_final: 0.8812 (t80) REVERT: J 134 PHE cc_start: 0.8518 (m-80) cc_final: 0.8209 (m-10) REVERT: J 157 ILE cc_start: 0.9797 (pt) cc_final: 0.9295 (pt) REVERT: K 20 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8599 (mmt180) REVERT: K 21 ILE cc_start: 0.9188 (mt) cc_final: 0.8873 (mt) REVERT: K 51 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8882 (tm-30) REVERT: K 52 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9044 (mm-40) REVERT: K 89 MET cc_start: 0.9649 (mtt) cc_final: 0.9157 (mtp) REVERT: K 94 LYS cc_start: 0.9586 (tttt) cc_final: 0.9378 (ttmm) REVERT: K 134 PHE cc_start: 0.8874 (m-80) cc_final: 0.8324 (m-10) REVERT: K 158 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8851 (mt-10) REVERT: L 39 ASN cc_start: 0.9042 (t0) cc_final: 0.8439 (t0) REVERT: L 51 GLU cc_start: 0.8858 (tm-30) cc_final: 0.7668 (tm-30) REVERT: L 52 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8893 (mm-40) REVERT: L 89 MET cc_start: 0.9519 (mtt) cc_final: 0.9232 (mtp) REVERT: L 113 HIS cc_start: 0.9375 (m-70) cc_final: 0.8724 (m-70) REVERT: L 134 PHE cc_start: 0.8706 (m-80) cc_final: 0.8149 (m-10) REVERT: L 135 ILE cc_start: 0.9164 (mp) cc_final: 0.8954 (mm) REVERT: L 162 PHE cc_start: 0.9528 (m-80) cc_final: 0.9256 (m-80) REVERT: M 20 ARG cc_start: 0.9127 (mmm160) cc_final: 0.8887 (mmt180) REVERT: M 21 ILE cc_start: 0.8851 (mt) cc_final: 0.8561 (mt) REVERT: M 46 ILE cc_start: 0.9712 (mt) cc_final: 0.9439 (tt) REVERT: M 51 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8766 (tm-30) REVERT: M 52 GLN cc_start: 0.9424 (mm-40) cc_final: 0.9090 (mm-40) REVERT: M 89 MET cc_start: 0.9414 (mtt) cc_final: 0.9212 (mtp) REVERT: M 134 PHE cc_start: 0.8307 (m-80) cc_final: 0.7805 (m-10) REVERT: M 157 ILE cc_start: 0.9728 (pt) cc_final: 0.9294 (pt) REVERT: M 162 PHE cc_start: 0.9594 (m-80) cc_final: 0.9282 (m-80) REVERT: N 48 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8283 (ttm110) REVERT: N 51 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8611 (tm-30) REVERT: N 52 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8920 (mm-40) REVERT: N 89 MET cc_start: 0.9651 (mtt) cc_final: 0.9357 (mtp) REVERT: N 94 LYS cc_start: 0.9620 (tttt) cc_final: 0.9236 (tppt) REVERT: N 99 TYR cc_start: 0.8913 (t80) cc_final: 0.8615 (t80) REVERT: N 134 PHE cc_start: 0.8727 (m-80) cc_final: 0.8369 (m-80) REVERT: P 21 ILE cc_start: 0.9029 (mt) cc_final: 0.8702 (mt) REVERT: P 36 ILE cc_start: 0.9727 (mm) cc_final: 0.9460 (tt) REVERT: P 39 ASN cc_start: 0.9227 (t0) cc_final: 0.8439 (t0) REVERT: P 51 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8662 (tm-30) REVERT: P 77 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8482 (ptmm) REVERT: P 94 LYS cc_start: 0.9654 (mtpt) cc_final: 0.9105 (tptt) REVERT: P 120 MET cc_start: 0.7893 (ppp) cc_final: 0.7512 (ppp) REVERT: P 134 PHE cc_start: 0.8612 (m-80) cc_final: 0.8234 (m-10) REVERT: P 162 PHE cc_start: 0.9413 (m-80) cc_final: 0.9149 (m-80) REVERT: R 39 ASN cc_start: 0.9266 (t0) cc_final: 0.8653 (t0) REVERT: R 43 MET cc_start: 0.9043 (tpp) cc_final: 0.8838 (tpp) REVERT: R 89 MET cc_start: 0.9511 (mtt) cc_final: 0.9179 (mtp) REVERT: R 113 HIS cc_start: 0.9451 (m-70) cc_final: 0.8834 (m-70) REVERT: R 134 PHE cc_start: 0.8842 (m-80) cc_final: 0.8414 (m-10) REVERT: T 21 ILE cc_start: 0.9093 (mt) cc_final: 0.8763 (mt) REVERT: T 99 TYR cc_start: 0.9049 (t80) cc_final: 0.8775 (t80) REVERT: T 113 HIS cc_start: 0.9430 (m-70) cc_final: 0.9001 (m-70) REVERT: T 134 PHE cc_start: 0.8391 (m-80) cc_final: 0.7808 (m-10) REVERT: T 162 PHE cc_start: 0.9208 (m-80) cc_final: 0.8913 (m-80) REVERT: a 35 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8576 (ttpp) REVERT: a 136 GLN cc_start: 0.9372 (mt0) cc_final: 0.8759 (mt0) REVERT: a 194 TYR cc_start: 0.9396 (m-80) cc_final: 0.9190 (m-80) REVERT: a 202 ARG cc_start: 0.9335 (mtm-85) cc_final: 0.8995 (mtm-85) REVERT: b 113 MET cc_start: 0.8898 (pmm) cc_final: 0.8539 (tmm) REVERT: b 127 LYS cc_start: 0.9583 (pttp) cc_final: 0.9145 (pttp) REVERT: b 171 LYS cc_start: 0.9088 (pttp) cc_final: 0.8733 (tptp) REVERT: c 35 LYS cc_start: 0.9065 (ptmm) cc_final: 0.8854 (ptmm) REVERT: c 127 LYS cc_start: 0.9552 (pttp) cc_final: 0.9332 (pttp) REVERT: c 171 LYS cc_start: 0.9146 (pttp) cc_final: 0.8919 (tptp) REVERT: c 199 ASP cc_start: 0.9198 (p0) cc_final: 0.8910 (p0) REVERT: d 125 GLN cc_start: 0.9333 (mt0) cc_final: 0.9080 (mm-40) REVERT: e 113 MET cc_start: 0.9015 (pmm) cc_final: 0.8772 (tmm) REVERT: e 125 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9174 (mm-40) REVERT: e 127 LYS cc_start: 0.9259 (pttp) cc_final: 0.9042 (pttp) REVERT: e 136 GLN cc_start: 0.9245 (mt0) cc_final: 0.8650 (mt0) REVERT: e 140 VAL cc_start: 0.8527 (t) cc_final: 0.8291 (p) REVERT: e 199 ASP cc_start: 0.9066 (p0) cc_final: 0.8219 (p0) REVERT: e 200 ILE cc_start: 0.9167 (mt) cc_final: 0.8908 (mm) REVERT: f 39 GLN cc_start: 0.9243 (mt0) cc_final: 0.8908 (mm-40) REVERT: f 59 MET cc_start: 0.9170 (mmm) cc_final: 0.8105 (mmm) REVERT: f 125 GLN cc_start: 0.9551 (mt0) cc_final: 0.9172 (pt0) REVERT: f 127 LYS cc_start: 0.9613 (pttp) cc_final: 0.9263 (pttp) REVERT: f 135 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9133 (mt-10) REVERT: g 35 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8727 (ptmm) REVERT: g 171 LYS cc_start: 0.9179 (pttp) cc_final: 0.8785 (tptp) REVERT: h 38 GLN cc_start: 0.9010 (tp40) cc_final: 0.8253 (tp-100) REVERT: h 125 GLN cc_start: 0.9358 (mt0) cc_final: 0.8995 (pt0) REVERT: h 127 LYS cc_start: 0.9533 (pttp) cc_final: 0.9286 (pttm) REVERT: i 194 TYR cc_start: 0.9460 (m-80) cc_final: 0.9237 (m-80) REVERT: i 202 ARG cc_start: 0.9207 (mtm-85) cc_final: 0.8933 (mtm-85) REVERT: j 35 LYS cc_start: 0.8855 (ptmm) cc_final: 0.8607 (ptmm) REVERT: j 39 GLN cc_start: 0.9239 (mt0) cc_final: 0.8946 (mm-40) REVERT: j 121 GLU cc_start: 0.9215 (mp0) cc_final: 0.8616 (tp30) REVERT: j 127 LYS cc_start: 0.9307 (pttp) cc_final: 0.9006 (pttm) REVERT: j 171 LYS cc_start: 0.9003 (pttp) cc_final: 0.8481 (tppt) REVERT: j 200 ILE cc_start: 0.8930 (mt) cc_final: 0.8674 (tt) REVERT: k 38 GLN cc_start: 0.8760 (tp40) cc_final: 0.8471 (tp-100) REVERT: k 116 LYS cc_start: 0.9661 (mttt) cc_final: 0.9142 (mtpt) REVERT: k 125 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8965 (mm-40) REVERT: k 171 LYS cc_start: 0.9073 (pttp) cc_final: 0.8724 (tptp) REVERT: k 194 TYR cc_start: 0.9433 (m-80) cc_final: 0.9231 (m-80) REVERT: k 199 ASP cc_start: 0.8960 (p0) cc_final: 0.8709 (p0) REVERT: l 127 LYS cc_start: 0.9486 (pttp) cc_final: 0.9117 (ptpp) REVERT: l 171 LYS cc_start: 0.9119 (pttp) cc_final: 0.8798 (tptp) REVERT: m 35 LYS cc_start: 0.9035 (ptmm) cc_final: 0.8635 (ptmm) REVERT: m 82 LEU cc_start: 0.9759 (tp) cc_final: 0.9508 (tp) REVERT: m 125 GLN cc_start: 0.9671 (mt0) cc_final: 0.9435 (mm-40) REVERT: m 127 LYS cc_start: 0.9534 (pttp) cc_final: 0.9099 (pttt) REVERT: n 125 GLN cc_start: 0.8846 (mp10) cc_final: 0.8635 (mm-40) REVERT: n 135 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9026 (mp0) REVERT: n 171 LYS cc_start: 0.9109 (pttp) cc_final: 0.8729 (tptp) REVERT: n 194 TYR cc_start: 0.9511 (m-80) cc_final: 0.9227 (m-80) REVERT: p 35 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8536 (ptmm) REVERT: p 125 GLN cc_start: 0.9297 (mp10) cc_final: 0.9021 (mm-40) REVERT: p 127 LYS cc_start: 0.9592 (pttp) cc_final: 0.9085 (pttp) REVERT: p 171 LYS cc_start: 0.9065 (pttp) cc_final: 0.8775 (tptp) REVERT: p 202 ARG cc_start: 0.9453 (mtm-85) cc_final: 0.9166 (mtm-85) REVERT: r 127 LYS cc_start: 0.8918 (pttp) cc_final: 0.8709 (pttp) REVERT: r 195 LYS cc_start: 0.9632 (tppp) cc_final: 0.9405 (tptp) REVERT: t 21 LYS cc_start: 0.9407 (mttt) cc_final: 0.8804 (tmtt) REVERT: t 38 GLN cc_start: 0.9218 (tp40) cc_final: 0.8648 (tp40) REVERT: t 127 LYS cc_start: 0.9697 (pttp) cc_final: 0.9257 (pttt) REVERT: t 171 LYS cc_start: 0.9135 (pttp) cc_final: 0.8763 (tptp) REVERT: t 194 TYR cc_start: 0.9335 (m-80) cc_final: 0.9014 (m-80) outliers start: 1 outliers final: 1 residues processed: 1737 average time/residue: 0.6254 time to fit residues: 1734.8249 Evaluate side-chains 1272 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1271 time to evaluate : 4.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 186 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 539 optimal weight: 50.0000 chunk 484 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 500 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 chunk 580 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 112 HIS C 30 HIS C 112 HIS E 30 HIS E 112 HIS E 114 ASN F 112 HIS G 52 GLN G 65 HIS G 112 HIS H 30 HIS H 113 HIS I 30 HIS I 112 HIS J 112 HIS K 30 HIS K 112 HIS L 30 HIS L 112 HIS M 30 HIS M 79 ASN M 112 HIS N 30 HIS N 112 HIS P 112 HIS R 30 HIS R 112 HIS ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 HIS a 30 ASN a 180 HIS b 30 ASN b 180 HIS c 30 ASN c 57 ASN d 30 ASN d 39 GLN e 39 GLN e 61 ASN f 30 ASN g 30 ASN g 39 GLN g 136 GLN h 30 ASN h 39 GLN i 30 ASN i 39 GLN i 57 ASN i 180 HIS k 30 ASN k 38 GLN l 30 ASN l 39 GLN m 30 ASN n 39 GLN n 57 ASN n 136 GLN p 39 GLN p 136 GLN p 180 HIS r 30 ASN r 39 GLN r 57 ASN r 180 HIS t 30 ASN t 39 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 58327 Z= 0.262 Angle : 0.763 9.730 81125 Z= 0.429 Chirality : 0.043 0.184 9340 Planarity : 0.006 0.058 8642 Dihedral : 17.459 70.169 11967 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.16 % Allowed : 15.21 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 5950 helix: 0.11 (0.07), residues: 4318 sheet: -0.83 (0.31), residues: 204 loop : -2.78 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 117 HIS 0.008 0.001 HIS P 65 PHE 0.045 0.002 PHE K 162 TYR 0.023 0.002 TYR H 17 ARG 0.011 0.001 ARG F 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1526 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9032 (tpp) cc_final: 0.8828 (mmm) REVERT: A 51 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 52 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8658 (mm-40) REVERT: A 99 TYR cc_start: 0.9059 (t80) cc_final: 0.8547 (t80) REVERT: A 120 MET cc_start: 0.8291 (ppp) cc_final: 0.7734 (ppp) REVERT: A 140 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8154 (ttp-110) REVERT: A 158 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 162 PHE cc_start: 0.9598 (m-80) cc_final: 0.9099 (m-80) REVERT: B 51 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 73 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8646 (tm-30) REVERT: B 84 TYR cc_start: 0.8609 (m-80) cc_final: 0.8253 (m-80) REVERT: B 99 TYR cc_start: 0.9083 (t80) cc_final: 0.8282 (t80) REVERT: B 152 LYS cc_start: 0.9731 (ptmm) cc_final: 0.9449 (pttp) REVERT: B 158 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8596 (mt-10) REVERT: C 39 ASN cc_start: 0.9103 (t0) cc_final: 0.8655 (t0) REVERT: C 51 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 52 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8720 (mm-40) REVERT: C 89 MET cc_start: 0.9368 (mtm) cc_final: 0.8750 (mtm) REVERT: C 110 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8934 (mm-30) REVERT: C 134 PHE cc_start: 0.7934 (m-80) cc_final: 0.7670 (m-10) REVERT: C 140 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8497 (ttp-110) REVERT: C 162 PHE cc_start: 0.9402 (m-80) cc_final: 0.9144 (m-80) REVERT: D 20 ARG cc_start: 0.8981 (mmm160) cc_final: 0.8445 (mmt180) REVERT: D 21 ILE cc_start: 0.9235 (mt) cc_final: 0.8927 (mt) REVERT: D 39 ASN cc_start: 0.9357 (t0) cc_final: 0.9090 (t0) REVERT: D 46 ILE cc_start: 0.9847 (mt) cc_final: 0.9585 (tt) REVERT: D 73 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 89 MET cc_start: 0.9464 (mtp) cc_final: 0.9008 (mtp) REVERT: D 120 MET cc_start: 0.8503 (ppp) cc_final: 0.7719 (ppp) REVERT: D 134 PHE cc_start: 0.8543 (m-80) cc_final: 0.8255 (m-10) REVERT: D 140 ARG cc_start: 0.8982 (ttp-110) cc_final: 0.8646 (ttp-110) REVERT: D 158 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8751 (mt-10) REVERT: E 17 TYR cc_start: 0.9092 (t80) cc_final: 0.8741 (t80) REVERT: E 21 ILE cc_start: 0.9162 (mt) cc_final: 0.8816 (mt) REVERT: E 51 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8761 (tm-30) REVERT: E 52 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8818 (mm-40) REVERT: E 110 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8681 (mt-10) REVERT: E 140 ARG cc_start: 0.8817 (ttp-110) cc_final: 0.8110 (mtm110) REVERT: E 162 PHE cc_start: 0.9604 (m-80) cc_final: 0.9283 (m-80) REVERT: F 27 THR cc_start: 0.8899 (m) cc_final: 0.8547 (m) REVERT: F 44 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8350 (mtm-85) REVERT: F 51 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 52 GLN cc_start: 0.9452 (mm-40) cc_final: 0.8881 (mm-40) REVERT: F 55 TYR cc_start: 0.9130 (t80) cc_final: 0.8927 (t80) REVERT: F 77 LYS cc_start: 0.8503 (ttpp) cc_final: 0.7263 (ttpp) REVERT: F 134 PHE cc_start: 0.8551 (m-80) cc_final: 0.8243 (m-10) REVERT: F 140 ARG cc_start: 0.8771 (ttp-110) cc_final: 0.8310 (ttp-110) REVERT: F 162 PHE cc_start: 0.9578 (m-80) cc_final: 0.9187 (m-80) REVERT: G 27 THR cc_start: 0.9034 (m) cc_final: 0.8619 (p) REVERT: G 39 ASN cc_start: 0.9395 (t0) cc_final: 0.9101 (t0) REVERT: G 99 TYR cc_start: 0.9324 (t80) cc_final: 0.8818 (t80) REVERT: G 120 MET cc_start: 0.8167 (ppp) cc_final: 0.7779 (ppp) REVERT: G 134 PHE cc_start: 0.8475 (m-80) cc_final: 0.8168 (m-10) REVERT: H 36 ILE cc_start: 0.9422 (pt) cc_final: 0.9134 (pt) REVERT: H 39 ASN cc_start: 0.9195 (t0) cc_final: 0.8670 (t0) REVERT: H 48 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8300 (ttm110) REVERT: H 89 MET cc_start: 0.9456 (mtt) cc_final: 0.8748 (mtm) REVERT: H 134 PHE cc_start: 0.8378 (m-80) cc_final: 0.7845 (m-10) REVERT: H 140 ARG cc_start: 0.9033 (ttp-110) cc_final: 0.8754 (ttp-110) REVERT: I 21 ILE cc_start: 0.9053 (mt) cc_final: 0.8698 (mt) REVERT: I 51 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8645 (tm-30) REVERT: I 52 GLN cc_start: 0.9383 (mm-40) cc_final: 0.8931 (mm-40) REVERT: I 84 TYR cc_start: 0.8757 (m-80) cc_final: 0.8193 (m-80) REVERT: I 89 MET cc_start: 0.9630 (mtt) cc_final: 0.9173 (mtm) REVERT: I 94 LYS cc_start: 0.9539 (ttpt) cc_final: 0.9077 (tptt) REVERT: I 113 HIS cc_start: 0.9077 (m-70) cc_final: 0.8671 (m90) REVERT: I 134 PHE cc_start: 0.8730 (m-80) cc_final: 0.8169 (m-10) REVERT: I 158 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8614 (mt-10) REVERT: I 162 PHE cc_start: 0.9536 (m-80) cc_final: 0.9110 (m-80) REVERT: J 21 ILE cc_start: 0.8981 (mt) cc_final: 0.8636 (mt) REVERT: J 53 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8662 (mt-10) REVERT: J 74 ILE cc_start: 0.9678 (mm) cc_final: 0.9217 (mm) REVERT: J 78 TYR cc_start: 0.8977 (m-10) cc_final: 0.8759 (m-10) REVERT: J 89 MET cc_start: 0.9636 (mtt) cc_final: 0.9264 (mtp) REVERT: J 99 TYR cc_start: 0.9088 (t80) cc_final: 0.7887 (t80) REVERT: J 120 MET cc_start: 0.7300 (ppp) cc_final: 0.6435 (ppp) REVERT: J 134 PHE cc_start: 0.8464 (m-80) cc_final: 0.8153 (m-10) REVERT: J 135 ILE cc_start: 0.8635 (mp) cc_final: 0.8415 (mm) REVERT: J 140 ARG cc_start: 0.8962 (ttp-110) cc_final: 0.8613 (ttp-110) REVERT: J 144 LYS cc_start: 0.9037 (tppt) cc_final: 0.8809 (tppt) REVERT: K 20 ARG cc_start: 0.9104 (mmm160) cc_final: 0.8755 (mmt180) REVERT: K 21 ILE cc_start: 0.9131 (mt) cc_final: 0.8854 (mt) REVERT: K 39 ASN cc_start: 0.9157 (t0) cc_final: 0.8889 (t0) REVERT: K 51 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8941 (tm-30) REVERT: K 52 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9000 (mm-40) REVERT: K 89 MET cc_start: 0.9643 (mtt) cc_final: 0.9148 (mtp) REVERT: K 134 PHE cc_start: 0.8884 (m-80) cc_final: 0.8440 (m-10) REVERT: K 140 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8107 (ttp-110) REVERT: K 162 PHE cc_start: 0.9250 (m-80) cc_final: 0.8750 (m-80) REVERT: L 39 ASN cc_start: 0.8905 (t0) cc_final: 0.8297 (t0) REVERT: L 89 MET cc_start: 0.9529 (mtt) cc_final: 0.9276 (mtp) REVERT: L 113 HIS cc_start: 0.9051 (m-70) cc_final: 0.8813 (m-70) REVERT: L 134 PHE cc_start: 0.8662 (m-80) cc_final: 0.8351 (m-10) REVERT: L 135 ILE cc_start: 0.8679 (mp) cc_final: 0.8431 (mm) REVERT: L 140 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.8313 (ttp-110) REVERT: L 147 THR cc_start: 0.9010 (p) cc_final: 0.8800 (t) REVERT: L 162 PHE cc_start: 0.9602 (m-80) cc_final: 0.9188 (m-80) REVERT: M 20 ARG cc_start: 0.9194 (mmm160) cc_final: 0.8820 (mmt180) REVERT: M 39 ASN cc_start: 0.9118 (t0) cc_final: 0.8680 (t0) REVERT: M 43 MET cc_start: 0.9418 (tpp) cc_final: 0.9182 (mmm) REVERT: M 51 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8823 (tm-30) REVERT: M 52 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9113 (mm-40) REVERT: M 134 PHE cc_start: 0.8403 (m-80) cc_final: 0.8113 (m-10) REVERT: M 158 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8635 (mt-10) REVERT: M 162 PHE cc_start: 0.9536 (m-80) cc_final: 0.9255 (m-80) REVERT: N 39 ASN cc_start: 0.9234 (t0) cc_final: 0.8797 (t0) REVERT: N 51 GLU cc_start: 0.9009 (tm-30) cc_final: 0.7761 (tm-30) REVERT: N 52 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8961 (mm-40) REVERT: N 89 MET cc_start: 0.9646 (mtt) cc_final: 0.9282 (mtp) REVERT: N 94 LYS cc_start: 0.9587 (tttt) cc_final: 0.9178 (tppt) REVERT: N 110 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9034 (mt-10) REVERT: N 120 MET cc_start: 0.8491 (ppp) cc_final: 0.8076 (ppp) REVERT: N 144 LYS cc_start: 0.8846 (tppt) cc_final: 0.8579 (tppt) REVERT: P 48 ARG cc_start: 0.8837 (tpp80) cc_final: 0.8611 (tpp80) REVERT: P 94 LYS cc_start: 0.9639 (mtpt) cc_final: 0.9239 (ttmm) REVERT: P 162 PHE cc_start: 0.9527 (m-80) cc_final: 0.9270 (m-80) REVERT: R 39 ASN cc_start: 0.9187 (t0) cc_final: 0.8365 (t0) REVERT: R 48 ARG cc_start: 0.9126 (tpp80) cc_final: 0.8784 (tpp80) REVERT: R 51 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8795 (tm-30) REVERT: R 113 HIS cc_start: 0.9142 (m-70) cc_final: 0.8901 (m-70) REVERT: R 140 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8134 (ttp-110) REVERT: T 39 ASN cc_start: 0.9159 (t0) cc_final: 0.8924 (t0) REVERT: T 99 TYR cc_start: 0.9143 (t80) cc_final: 0.8554 (t80) REVERT: T 134 PHE cc_start: 0.8602 (m-80) cc_final: 0.8215 (m-10) REVERT: T 140 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8294 (ttp-110) REVERT: T 144 LYS cc_start: 0.8999 (tppt) cc_final: 0.8718 (tppt) REVERT: T 162 PHE cc_start: 0.9333 (m-80) cc_final: 0.8981 (m-80) REVERT: a 38 GLN cc_start: 0.9188 (tp40) cc_final: 0.8884 (tp40) REVERT: a 39 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8670 (mm-40) REVERT: a 136 GLN cc_start: 0.9236 (mt0) cc_final: 0.8830 (mt0) REVERT: a 194 TYR cc_start: 0.9382 (m-80) cc_final: 0.9117 (m-80) REVERT: b 59 MET cc_start: 0.9119 (mmp) cc_final: 0.8742 (mmp) REVERT: b 87 ILE cc_start: 0.9679 (mt) cc_final: 0.9322 (tt) REVERT: b 158 MET cc_start: 0.8869 (tpp) cc_final: 0.8353 (tpp) REVERT: b 187 PHE cc_start: 0.1677 (OUTLIER) cc_final: 0.1023 (m-80) REVERT: c 39 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8533 (mm-40) REVERT: c 127 LYS cc_start: 0.9603 (pttp) cc_final: 0.9369 (pttp) REVERT: c 140 VAL cc_start: 0.8442 (t) cc_final: 0.8229 (p) REVERT: c 199 ASP cc_start: 0.9179 (p0) cc_final: 0.8849 (p0) REVERT: d 199 ASP cc_start: 0.9317 (p0) cc_final: 0.9112 (p0) REVERT: d 200 ILE cc_start: 0.8968 (mm) cc_final: 0.8678 (tt) REVERT: e 44 MET cc_start: 0.9084 (ttm) cc_final: 0.8857 (mtp) REVERT: e 59 MET cc_start: 0.9117 (mmm) cc_final: 0.8805 (mmm) REVERT: e 96 GLU cc_start: 0.8942 (mp0) cc_final: 0.8609 (mm-30) REVERT: e 125 GLN cc_start: 0.9338 (mm-40) cc_final: 0.9125 (mm-40) REVERT: e 140 VAL cc_start: 0.8697 (t) cc_final: 0.8460 (p) REVERT: e 186 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.6081 (m) REVERT: e 199 ASP cc_start: 0.9271 (p0) cc_final: 0.9030 (p0) REVERT: e 201 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8251 (mm-30) REVERT: f 42 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7128 (mt-10) REVERT: f 59 MET cc_start: 0.9082 (mmm) cc_final: 0.7895 (mmm) REVERT: f 125 GLN cc_start: 0.9271 (mt0) cc_final: 0.8975 (pt0) REVERT: f 158 MET cc_start: 0.9339 (tpp) cc_final: 0.9024 (tpp) REVERT: f 173 LYS cc_start: 0.9049 (ptpt) cc_final: 0.8791 (mttp) REVERT: g 39 GLN cc_start: 0.8628 (mm110) cc_final: 0.8415 (mm-40) REVERT: g 42 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6779 (mt-10) REVERT: g 158 MET cc_start: 0.8994 (tpp) cc_final: 0.8482 (tpp) REVERT: g 171 LYS cc_start: 0.9150 (pttp) cc_final: 0.8865 (tptp) REVERT: g 186 THR cc_start: 0.5575 (OUTLIER) cc_final: 0.5369 (m) REVERT: h 59 MET cc_start: 0.9049 (mmp) cc_final: 0.8500 (mmp) REVERT: h 156 THR cc_start: 0.9395 (t) cc_final: 0.9177 (p) REVERT: h 158 MET cc_start: 0.8914 (tpp) cc_final: 0.8153 (tpp) REVERT: i 39 GLN cc_start: 0.9040 (mm110) cc_final: 0.8383 (mm-40) REVERT: i 197 LEU cc_start: 0.9312 (tp) cc_final: 0.9041 (tp) REVERT: i 201 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8046 (mm-30) REVERT: j 126 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9334 (tp) REVERT: j 127 LYS cc_start: 0.9412 (pttp) cc_final: 0.9078 (pttp) REVERT: j 171 LYS cc_start: 0.8847 (pttp) cc_final: 0.8480 (tppt) REVERT: j 194 TYR cc_start: 0.9077 (m-80) cc_final: 0.8818 (m-80) REVERT: k 38 GLN cc_start: 0.8975 (tp-100) cc_final: 0.7236 (tp-100) REVERT: k 39 GLN cc_start: 0.9001 (mm110) cc_final: 0.8095 (mm110) REVERT: k 116 LYS cc_start: 0.9703 (mttt) cc_final: 0.9440 (mtpt) REVERT: k 126 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9195 (tt) REVERT: k 171 LYS cc_start: 0.9083 (pttp) cc_final: 0.8808 (tptp) REVERT: l 96 GLU cc_start: 0.8909 (mp0) cc_final: 0.8518 (mm-30) REVERT: l 126 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9135 (tt) REVERT: l 171 LYS cc_start: 0.9096 (pttp) cc_final: 0.8891 (tptp) REVERT: l 187 PHE cc_start: -0.0172 (OUTLIER) cc_final: -0.1337 (m-80) REVERT: m 39 GLN cc_start: 0.7790 (pp30) cc_final: 0.7148 (pp30) REVERT: m 82 LEU cc_start: 0.9772 (tp) cc_final: 0.9542 (tp) REVERT: m 96 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8743 (mt-10) REVERT: m 121 GLU cc_start: 0.9230 (mp0) cc_final: 0.8761 (tp30) REVERT: m 125 GLN cc_start: 0.9414 (mt0) cc_final: 0.8435 (mm110) REVERT: m 170 MET cc_start: 0.9250 (ptp) cc_final: 0.8668 (mmp) REVERT: m 199 ASP cc_start: 0.9098 (p0) cc_final: 0.8857 (p0) REVERT: n 39 GLN cc_start: 0.8688 (mm110) cc_final: 0.8336 (mm110) REVERT: n 42 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6768 (mt-10) REVERT: n 59 MET cc_start: 0.8887 (mmp) cc_final: 0.7215 (mmm) REVERT: n 126 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9345 (pp) REVERT: n 169 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7295 (pp) REVERT: n 202 ARG cc_start: 0.9310 (mtm-85) cc_final: 0.8978 (ptp-170) REVERT: p 11 ASP cc_start: 0.8562 (m-30) cc_final: 0.8030 (m-30) REVERT: p 82 LEU cc_start: 0.9703 (tp) cc_final: 0.9422 (tp) REVERT: r 158 MET cc_start: 0.8964 (tpp) cc_final: 0.8673 (tpp) REVERT: r 186 THR cc_start: 0.4024 (OUTLIER) cc_final: 0.3811 (m) REVERT: r 187 PHE cc_start: -0.0396 (OUTLIER) cc_final: -0.1184 (m-80) REVERT: t 21 LYS cc_start: 0.9408 (mttt) cc_final: 0.8812 (tmtt) REVERT: t 38 GLN cc_start: 0.9380 (tp40) cc_final: 0.8606 (tp-100) REVERT: t 82 LEU cc_start: 0.9851 (tp) cc_final: 0.9529 (tp) REVERT: t 194 TYR cc_start: 0.9228 (m-80) cc_final: 0.8920 (m-80) outliers start: 108 outliers final: 51 residues processed: 1575 average time/residue: 0.6381 time to fit residues: 1620.2187 Evaluate side-chains 1332 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1270 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain a residue 180 HIS Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 187 PHE Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain e residue 27 ILE Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 186 THR Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain k residue 126 LEU Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain l residue 187 PHE Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 200 ILE Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 169 LEU Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 186 THR Chi-restraints excluded: chain r residue 186 THR Chi-restraints excluded: chain r residue 187 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 482 optimal weight: 8.9990 chunk 395 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 581 optimal weight: 10.0000 chunk 627 optimal weight: 5.9990 chunk 517 optimal weight: 8.9990 chunk 576 optimal weight: 0.0170 chunk 198 optimal weight: 6.9990 chunk 466 optimal weight: 20.0000 overall best weight: 3.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 ASN E 114 ASN F 65 HIS G 52 GLN H 112 HIS I 114 ASN J 24 ASN P 114 ASN b 57 ASN c 136 GLN d 39 GLN d 180 HIS e 30 ASN f 39 GLN f 136 GLN f 180 HIS g 136 GLN h 39 GLN i 136 GLN j 43 ASN l 39 GLN l 57 ASN n 30 ASN ** n 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 180 HIS p 39 GLN r 39 GLN t 39 GLN t 57 ASN t 136 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 58327 Z= 0.231 Angle : 0.757 13.594 81125 Z= 0.419 Chirality : 0.042 0.200 9340 Planarity : 0.005 0.066 8642 Dihedral : 17.314 83.955 11967 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.40 % Allowed : 18.61 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5950 helix: 0.59 (0.08), residues: 4335 sheet: -0.34 (0.30), residues: 204 loop : -2.56 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 117 HIS 0.011 0.001 HIS i 180 PHE 0.033 0.002 PHE G 162 TYR 0.032 0.002 TYR G 17 ARG 0.011 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1445 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9414 (pt) cc_final: 0.9081 (mt) REVERT: A 39 ASN cc_start: 0.9211 (t0) cc_final: 0.8875 (t0) REVERT: A 51 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 52 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8647 (mm-40) REVERT: A 77 LYS cc_start: 0.8573 (ttpp) cc_final: 0.7680 (ttpp) REVERT: A 78 TYR cc_start: 0.8886 (m-10) cc_final: 0.8594 (m-10) REVERT: A 89 MET cc_start: 0.9223 (mtm) cc_final: 0.8673 (mtm) REVERT: A 110 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8656 (mt-10) REVERT: A 120 MET cc_start: 0.8303 (ppp) cc_final: 0.7960 (ppp) REVERT: A 158 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8323 (mt-10) REVERT: A 162 PHE cc_start: 0.9418 (m-80) cc_final: 0.8997 (m-80) REVERT: B 39 ASN cc_start: 0.9241 (t0) cc_final: 0.8690 (t0) REVERT: B 43 MET cc_start: 0.8872 (mmm) cc_final: 0.8611 (mmm) REVERT: B 51 GLU cc_start: 0.9086 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 52 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8331 (mm-40) REVERT: B 73 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8602 (tm-30) REVERT: B 99 TYR cc_start: 0.8915 (t80) cc_final: 0.8703 (t80) REVERT: B 134 PHE cc_start: 0.8431 (m-80) cc_final: 0.8157 (m-80) REVERT: B 158 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8699 (mt-10) REVERT: C 39 ASN cc_start: 0.8917 (t0) cc_final: 0.8050 (t0) REVERT: C 51 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 52 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8582 (mm-40) REVERT: C 89 MET cc_start: 0.9426 (mtm) cc_final: 0.9180 (mtm) REVERT: C 110 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8880 (mm-30) REVERT: C 134 PHE cc_start: 0.8246 (m-80) cc_final: 0.7941 (m-10) REVERT: C 152 LYS cc_start: 0.9732 (ttpp) cc_final: 0.9306 (pttp) REVERT: C 162 PHE cc_start: 0.9453 (m-80) cc_final: 0.9127 (m-80) REVERT: C 163 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8752 (ptpp) REVERT: D 20 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8353 (mmt180) REVERT: D 21 ILE cc_start: 0.9135 (mt) cc_final: 0.8868 (mt) REVERT: D 39 ASN cc_start: 0.9268 (t0) cc_final: 0.8706 (t0) REVERT: D 43 MET cc_start: 0.9013 (mmm) cc_final: 0.8583 (mmm) REVERT: D 89 MET cc_start: 0.9417 (mtp) cc_final: 0.9024 (mtp) REVERT: D 134 PHE cc_start: 0.8412 (m-80) cc_final: 0.8129 (m-10) REVERT: D 158 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8830 (mt-10) REVERT: E 12 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8522 (t) REVERT: E 17 TYR cc_start: 0.9058 (t80) cc_final: 0.8658 (t80) REVERT: E 21 ILE cc_start: 0.9047 (mt) cc_final: 0.8589 (mt) REVERT: E 51 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8699 (tm-30) REVERT: E 52 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8887 (mm-40) REVERT: E 89 MET cc_start: 0.9443 (mtm) cc_final: 0.8763 (mtm) REVERT: E 110 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8612 (mt-10) REVERT: E 152 LYS cc_start: 0.9696 (ttpp) cc_final: 0.9382 (ptmm) REVERT: E 162 PHE cc_start: 0.9571 (m-80) cc_final: 0.9345 (m-80) REVERT: F 27 THR cc_start: 0.8713 (m) cc_final: 0.8229 (m) REVERT: F 39 ASN cc_start: 0.9127 (t0) cc_final: 0.8871 (t0) REVERT: F 48 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8474 (ttm110) REVERT: F 51 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8737 (tm-30) REVERT: F 52 GLN cc_start: 0.9479 (mm-40) cc_final: 0.8903 (mm-40) REVERT: F 53 GLU cc_start: 0.8436 (tt0) cc_final: 0.8056 (tm-30) REVERT: F 55 TYR cc_start: 0.9128 (t80) cc_final: 0.8905 (t80) REVERT: F 99 TYR cc_start: 0.9208 (t80) cc_final: 0.8307 (t80) REVERT: F 134 PHE cc_start: 0.8583 (m-80) cc_final: 0.8165 (m-10) REVERT: F 162 PHE cc_start: 0.9526 (m-80) cc_final: 0.8994 (m-80) REVERT: G 27 THR cc_start: 0.8988 (m) cc_final: 0.8551 (p) REVERT: G 34 LEU cc_start: 0.9368 (mm) cc_final: 0.9132 (mm) REVERT: G 99 TYR cc_start: 0.9329 (t80) cc_final: 0.8715 (t80) REVERT: G 162 PHE cc_start: 0.9242 (m-80) cc_final: 0.8984 (m-80) REVERT: H 89 MET cc_start: 0.9411 (mtt) cc_final: 0.8719 (mtm) REVERT: H 99 TYR cc_start: 0.9298 (t80) cc_final: 0.9081 (t80) REVERT: H 120 MET cc_start: 0.7572 (ppp) cc_final: 0.7009 (ppp) REVERT: H 134 PHE cc_start: 0.8283 (m-80) cc_final: 0.7876 (m-10) REVERT: H 140 ARG cc_start: 0.9019 (ttp-110) cc_final: 0.8769 (ttp-110) REVERT: H 144 LYS cc_start: 0.9144 (tppt) cc_final: 0.8884 (tppt) REVERT: I 21 ILE cc_start: 0.8883 (mt) cc_final: 0.8490 (mt) REVERT: I 39 ASN cc_start: 0.9156 (t0) cc_final: 0.8853 (t0) REVERT: I 44 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: I 51 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8601 (tm-30) REVERT: I 52 GLN cc_start: 0.9360 (mm-40) cc_final: 0.8807 (mm-40) REVERT: I 84 TYR cc_start: 0.8741 (m-80) cc_final: 0.8252 (m-80) REVERT: I 89 MET cc_start: 0.9605 (mtt) cc_final: 0.9166 (mtm) REVERT: I 113 HIS cc_start: 0.8999 (m-70) cc_final: 0.8609 (m90) REVERT: I 134 PHE cc_start: 0.8754 (m-80) cc_final: 0.8143 (m-10) REVERT: I 158 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8718 (mt-10) REVERT: I 159 ASP cc_start: 0.9629 (p0) cc_final: 0.9427 (p0) REVERT: I 162 PHE cc_start: 0.9499 (m-80) cc_final: 0.9113 (m-80) REVERT: J 21 ILE cc_start: 0.8908 (mt) cc_final: 0.8559 (mt) REVERT: J 39 ASN cc_start: 0.8816 (t0) cc_final: 0.8396 (t0) REVERT: J 43 MET cc_start: 0.9042 (mmm) cc_final: 0.8661 (mmm) REVERT: J 51 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: J 53 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8494 (mt-10) REVERT: J 74 ILE cc_start: 0.9697 (mm) cc_final: 0.9448 (mm) REVERT: J 99 TYR cc_start: 0.8986 (t80) cc_final: 0.8403 (t80) REVERT: J 134 PHE cc_start: 0.8492 (m-80) cc_final: 0.8223 (m-10) REVERT: J 140 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8637 (ttp-110) REVERT: J 144 LYS cc_start: 0.8976 (tppt) cc_final: 0.8744 (tppt) REVERT: J 158 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8769 (mt-10) REVERT: K 20 ARG cc_start: 0.9071 (mmm160) cc_final: 0.8621 (mmt180) REVERT: K 21 ILE cc_start: 0.9107 (mt) cc_final: 0.8810 (mt) REVERT: K 39 ASN cc_start: 0.9204 (t0) cc_final: 0.8859 (t0) REVERT: K 89 MET cc_start: 0.9626 (mtt) cc_final: 0.9135 (mtp) REVERT: K 110 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8278 (mt-10) REVERT: K 134 PHE cc_start: 0.8760 (m-80) cc_final: 0.8480 (m-10) REVERT: K 140 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8303 (ttp-110) REVERT: K 144 LYS cc_start: 0.8917 (tppt) cc_final: 0.8605 (tppt) REVERT: K 162 PHE cc_start: 0.9321 (m-80) cc_final: 0.9054 (m-80) REVERT: L 39 ASN cc_start: 0.8811 (t0) cc_final: 0.8198 (p0) REVERT: L 89 MET cc_start: 0.9482 (mtt) cc_final: 0.9225 (mtp) REVERT: L 110 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8611 (tt0) REVERT: L 113 HIS cc_start: 0.9057 (m-70) cc_final: 0.8820 (m-70) REVERT: L 134 PHE cc_start: 0.8598 (m-80) cc_final: 0.8396 (m-10) REVERT: L 144 LYS cc_start: 0.9076 (tppt) cc_final: 0.8838 (tppt) REVERT: L 152 LYS cc_start: 0.9641 (ttpp) cc_final: 0.9400 (pttp) REVERT: L 162 PHE cc_start: 0.9559 (m-80) cc_final: 0.9232 (m-80) REVERT: M 20 ARG cc_start: 0.9108 (mmm160) cc_final: 0.8703 (mmt180) REVERT: M 39 ASN cc_start: 0.8954 (t0) cc_final: 0.8544 (t0) REVERT: M 51 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8712 (tm-30) REVERT: M 52 GLN cc_start: 0.9448 (mm-40) cc_final: 0.8980 (mm-40) REVERT: M 89 MET cc_start: 0.9228 (mtm) cc_final: 0.8906 (mtm) REVERT: M 99 TYR cc_start: 0.9048 (t80) cc_final: 0.8596 (t80) REVERT: M 158 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8590 (mt-10) REVERT: M 162 PHE cc_start: 0.9391 (m-80) cc_final: 0.9184 (m-80) REVERT: N 39 ASN cc_start: 0.9068 (t0) cc_final: 0.8814 (t0) REVERT: N 43 MET cc_start: 0.9348 (mmm) cc_final: 0.8868 (mmm) REVERT: N 48 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8232 (ttm110) REVERT: N 89 MET cc_start: 0.9599 (mtt) cc_final: 0.9299 (mtp) REVERT: N 94 LYS cc_start: 0.9527 (tttt) cc_final: 0.9249 (ttmm) REVERT: N 110 GLU cc_start: 0.9221 (mm-30) cc_final: 0.9020 (mt-10) REVERT: N 120 MET cc_start: 0.8446 (ppp) cc_final: 0.8211 (ppp) REVERT: N 144 LYS cc_start: 0.8820 (tppt) cc_final: 0.8557 (tppt) REVERT: P 39 ASN cc_start: 0.9095 (t0) cc_final: 0.8124 (t0) REVERT: P 48 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8548 (tpp80) REVERT: P 113 HIS cc_start: 0.9034 (m-70) cc_final: 0.8675 (m-70) REVERT: P 162 PHE cc_start: 0.9503 (m-80) cc_final: 0.9069 (m-80) REVERT: R 39 ASN cc_start: 0.9029 (t0) cc_final: 0.8771 (t0) REVERT: R 113 HIS cc_start: 0.9070 (m-70) cc_final: 0.8785 (m-70) REVERT: R 140 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8354 (ttp-110) REVERT: R 159 ASP cc_start: 0.9513 (p0) cc_final: 0.9203 (p0) REVERT: T 94 LYS cc_start: 0.9362 (ttmm) cc_final: 0.9160 (ttmm) REVERT: T 99 TYR cc_start: 0.9128 (t80) cc_final: 0.8516 (t80) REVERT: T 134 PHE cc_start: 0.8617 (m-80) cc_final: 0.8299 (m-10) REVERT: T 162 PHE cc_start: 0.9363 (m-80) cc_final: 0.9015 (m-80) REVERT: a 39 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8734 (mm-40) REVERT: a 82 LEU cc_start: 0.9743 (tp) cc_final: 0.9450 (tp) REVERT: b 113 MET cc_start: 0.8547 (tmm) cc_final: 0.8161 (tmm) REVERT: b 158 MET cc_start: 0.9153 (tpp) cc_final: 0.8801 (tpp) REVERT: b 170 MET cc_start: 0.8811 (mtm) cc_final: 0.8163 (mmm) REVERT: b 173 LYS cc_start: 0.8851 (pttt) cc_final: 0.8613 (ptpt) REVERT: b 187 PHE cc_start: 0.1552 (OUTLIER) cc_final: 0.1070 (m-80) REVERT: c 158 MET cc_start: 0.8985 (tpp) cc_final: 0.8758 (tpp) REVERT: d 38 GLN cc_start: 0.8990 (tp40) cc_final: 0.8626 (tp40) REVERT: d 39 GLN cc_start: 0.9187 (mm110) cc_final: 0.8026 (mm-40) REVERT: d 59 MET cc_start: 0.9116 (mmp) cc_final: 0.7880 (mmp) REVERT: d 126 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9398 (tp) REVERT: e 59 MET cc_start: 0.9134 (mmm) cc_final: 0.8755 (mmm) REVERT: e 96 GLU cc_start: 0.8942 (mp0) cc_final: 0.8650 (mm-30) REVERT: e 140 VAL cc_start: 0.8691 (t) cc_final: 0.8469 (p) REVERT: e 158 MET cc_start: 0.9133 (tpp) cc_final: 0.8788 (tpp) REVERT: e 186 THR cc_start: 0.6202 (OUTLIER) cc_final: 0.5823 (m) REVERT: f 27 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9167 (tp) REVERT: f 59 MET cc_start: 0.9014 (mmm) cc_final: 0.7590 (mmm) REVERT: f 125 GLN cc_start: 0.9191 (mt0) cc_final: 0.8772 (pt0) REVERT: f 186 THR cc_start: 0.3912 (OUTLIER) cc_final: 0.3354 (m) REVERT: f 200 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8701 (tt) REVERT: g 144 HIS cc_start: 0.9333 (p-80) cc_final: 0.8896 (p-80) REVERT: g 158 MET cc_start: 0.9257 (tpp) cc_final: 0.8903 (tpp) REVERT: g 186 THR cc_start: 0.5439 (OUTLIER) cc_final: 0.5158 (m) REVERT: g 195 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8785 (mmmm) REVERT: h 21 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9255 (mtmm) REVERT: h 152 ASP cc_start: 0.9271 (m-30) cc_final: 0.8946 (m-30) REVERT: h 171 LYS cc_start: 0.8841 (pttm) cc_final: 0.8605 (pttm) REVERT: h 187 PHE cc_start: 0.0243 (OUTLIER) cc_final: -0.0269 (m-80) REVERT: h 199 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8658 (p0) REVERT: i 158 MET cc_start: 0.8612 (tpp) cc_final: 0.8275 (tpp) REVERT: i 186 THR cc_start: 0.5119 (OUTLIER) cc_final: 0.4623 (m) REVERT: i 201 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8112 (mm-30) REVERT: j 39 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8086 (mm110) REVERT: j 113 MET cc_start: 0.9015 (tpp) cc_final: 0.8414 (tpp) REVERT: j 116 LYS cc_start: 0.9644 (mtpt) cc_final: 0.9397 (mtmm) REVERT: j 126 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9251 (tp) REVERT: j 127 LYS cc_start: 0.9493 (pttp) cc_final: 0.9204 (pttp) REVERT: j 158 MET cc_start: 0.8918 (tpp) cc_final: 0.8665 (tpp) REVERT: k 39 GLN cc_start: 0.8728 (mm110) cc_final: 0.8308 (mm-40) REVERT: k 113 MET cc_start: 0.9234 (tpp) cc_final: 0.8834 (tpp) REVERT: k 158 MET cc_start: 0.8419 (tpp) cc_final: 0.8219 (tpp) REVERT: k 186 THR cc_start: 0.5525 (OUTLIER) cc_final: 0.4983 (m) REVERT: k 194 TYR cc_start: 0.9197 (m-80) cc_final: 0.8950 (m-80) REVERT: l 32 MET cc_start: 0.8714 (mmp) cc_final: 0.8512 (mmp) REVERT: l 96 GLU cc_start: 0.8932 (mp0) cc_final: 0.8485 (mm-30) REVERT: l 113 MET cc_start: 0.9015 (tpp) cc_final: 0.8567 (tpp) REVERT: l 126 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9171 (tt) REVERT: l 187 PHE cc_start: -0.0283 (OUTLIER) cc_final: -0.1263 (m-80) REVERT: l 202 ARG cc_start: 0.9051 (mtm-85) cc_final: 0.8695 (ptp-170) REVERT: m 82 LEU cc_start: 0.9762 (tp) cc_final: 0.9550 (tp) REVERT: m 96 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8742 (mt-10) REVERT: m 127 LYS cc_start: 0.9485 (pttp) cc_final: 0.9224 (pttp) REVERT: m 158 MET cc_start: 0.8611 (tpp) cc_final: 0.8219 (tpp) REVERT: m 202 ARG cc_start: 0.8615 (ptp-170) cc_final: 0.7971 (mtm-85) REVERT: n 126 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9335 (tp) REVERT: n 187 PHE cc_start: 0.0054 (OUTLIER) cc_final: -0.0221 (m-80) REVERT: n 202 ARG cc_start: 0.9178 (mtm-85) cc_final: 0.8812 (ptp-170) REVERT: p 82 LEU cc_start: 0.9694 (tp) cc_final: 0.9417 (tp) REVERT: r 187 PHE cc_start: -0.0942 (OUTLIER) cc_final: -0.1752 (m-80) REVERT: r 200 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8724 (tt) REVERT: t 38 GLN cc_start: 0.9377 (tp40) cc_final: 0.8957 (tp-100) REVERT: t 187 PHE cc_start: 0.0778 (OUTLIER) cc_final: -0.0369 (m-80) REVERT: t 194 TYR cc_start: 0.9224 (m-80) cc_final: 0.8837 (m-80) outliers start: 120 outliers final: 57 residues processed: 1505 average time/residue: 0.6481 time to fit residues: 1573.2149 Evaluate side-chains 1326 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1247 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 187 PHE Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain d residue 186 THR Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 186 THR Chi-restraints excluded: chain f residue 27 ILE Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 186 THR Chi-restraints excluded: chain f residue 200 ILE Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 187 PHE Chi-restraints excluded: chain h residue 198 GLU Chi-restraints excluded: chain h residue 199 ASP Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 186 THR Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 186 THR Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain l residue 187 PHE Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 187 PHE Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 187 PHE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 187 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 574 optimal weight: 7.9990 chunk 437 optimal weight: 30.0000 chunk 301 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 583 optimal weight: 7.9990 chunk 617 optimal weight: 30.0000 chunk 304 optimal weight: 8.9990 chunk 552 optimal weight: 40.0000 chunk 166 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 HIS a 39 GLN a 180 HIS f 39 GLN g 38 GLN g 57 ASN ** g 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 136 GLN h 39 GLN i 39 GLN i 180 HIS j 30 ASN j 39 GLN j 43 ASN l 39 GLN n 39 GLN n 43 ASN n 136 GLN p 30 ASN p 39 GLN r 38 GLN r 39 GLN t 39 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 58327 Z= 0.260 Angle : 0.770 13.908 81125 Z= 0.426 Chirality : 0.042 0.296 9340 Planarity : 0.005 0.058 8642 Dihedral : 17.271 81.516 11967 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.46 % Allowed : 20.25 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5950 helix: 0.73 (0.08), residues: 4335 sheet: -0.09 (0.31), residues: 204 loop : -2.48 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.015 0.001 HIS J 65 PHE 0.023 0.002 PHE G 162 TYR 0.029 0.002 TYR R 17 ARG 0.012 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1538 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1365 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8520 (tm-30) REVERT: A 52 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8653 (mm-40) REVERT: A 89 MET cc_start: 0.9408 (mtm) cc_final: 0.9149 (mtm) REVERT: A 120 MET cc_start: 0.8318 (ppp) cc_final: 0.8057 (ppp) REVERT: A 158 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 162 PHE cc_start: 0.9580 (m-80) cc_final: 0.9202 (m-80) REVERT: B 39 ASN cc_start: 0.9268 (t0) cc_final: 0.8731 (t0) REVERT: B 51 GLU cc_start: 0.9131 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 52 GLN cc_start: 0.9339 (mm-40) cc_final: 0.8285 (mm-40) REVERT: B 99 TYR cc_start: 0.9033 (t80) cc_final: 0.7588 (t80) REVERT: B 108 LEU cc_start: 0.9398 (pt) cc_final: 0.9115 (mt) REVERT: B 120 MET cc_start: 0.7157 (ppp) cc_final: 0.6628 (ppp) REVERT: B 157 ILE cc_start: 0.9812 (pt) cc_final: 0.9541 (pt) REVERT: C 39 ASN cc_start: 0.8717 (t0) cc_final: 0.8349 (t0) REVERT: C 51 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 52 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8707 (mm-40) REVERT: C 89 MET cc_start: 0.9445 (mtm) cc_final: 0.9125 (mtm) REVERT: C 134 PHE cc_start: 0.8188 (m-80) cc_final: 0.7895 (m-10) REVERT: C 161 LEU cc_start: 0.9268 (tt) cc_final: 0.8837 (tt) REVERT: C 162 PHE cc_start: 0.9460 (m-80) cc_final: 0.9097 (m-80) REVERT: C 163 LYS cc_start: 0.9218 (ptpp) cc_final: 0.8878 (ptpp) REVERT: D 20 ARG cc_start: 0.8909 (mmm160) cc_final: 0.8423 (mmt180) REVERT: D 39 ASN cc_start: 0.9252 (t0) cc_final: 0.8849 (t0) REVERT: D 41 GLU cc_start: 0.8852 (mp0) cc_final: 0.8590 (mm-30) REVERT: D 44 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: D 48 ARG cc_start: 0.9124 (tpp80) cc_final: 0.8890 (tpp80) REVERT: D 89 MET cc_start: 0.9425 (mtp) cc_final: 0.9006 (mtp) REVERT: D 94 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.8915 (ttmm) REVERT: D 134 PHE cc_start: 0.8346 (m-80) cc_final: 0.8084 (m-10) REVERT: D 158 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8849 (mt-10) REVERT: E 12 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8574 (t) REVERT: E 17 TYR cc_start: 0.9070 (t80) cc_final: 0.8677 (t80) REVERT: E 21 ILE cc_start: 0.9143 (mt) cc_final: 0.8814 (mt) REVERT: E 39 ASN cc_start: 0.8795 (t0) cc_final: 0.8179 (t0) REVERT: E 51 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8778 (tm-30) REVERT: E 52 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8846 (mm-40) REVERT: E 89 MET cc_start: 0.9499 (mtm) cc_final: 0.8820 (mtm) REVERT: E 110 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8817 (mm-30) REVERT: E 152 LYS cc_start: 0.9714 (ttpp) cc_final: 0.9394 (ptmm) REVERT: E 162 PHE cc_start: 0.9565 (m-80) cc_final: 0.9360 (m-80) REVERT: F 39 ASN cc_start: 0.9190 (t0) cc_final: 0.8815 (t0) REVERT: F 51 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8876 (tm-30) REVERT: F 52 GLN cc_start: 0.9462 (mm-40) cc_final: 0.8880 (mm-40) REVERT: F 55 TYR cc_start: 0.9113 (t80) cc_final: 0.8886 (t80) REVERT: F 134 PHE cc_start: 0.8611 (m-80) cc_final: 0.8271 (m-10) REVERT: F 162 PHE cc_start: 0.9478 (m-80) cc_final: 0.8968 (m-80) REVERT: G 27 THR cc_start: 0.9061 (m) cc_final: 0.8584 (p) REVERT: G 34 LEU cc_start: 0.9358 (mm) cc_final: 0.9147 (mm) REVERT: G 39 ASN cc_start: 0.9183 (t0) cc_final: 0.8911 (t0) REVERT: G 99 TYR cc_start: 0.9319 (t80) cc_final: 0.8851 (t80) REVERT: G 111 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9421 (tp) REVERT: G 162 PHE cc_start: 0.9301 (m-80) cc_final: 0.8988 (m-80) REVERT: H 43 MET cc_start: 0.9268 (mmm) cc_final: 0.9019 (mmm) REVERT: H 48 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8476 (ttm-80) REVERT: H 73 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8538 (pp30) REVERT: H 74 ILE cc_start: 0.9563 (mm) cc_final: 0.9357 (mm) REVERT: H 77 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8823 (mtmm) REVERT: H 78 TYR cc_start: 0.9025 (m-10) cc_final: 0.8555 (m-10) REVERT: H 89 MET cc_start: 0.9377 (mtt) cc_final: 0.8669 (mtm) REVERT: H 99 TYR cc_start: 0.9313 (t80) cc_final: 0.9090 (t80) REVERT: H 134 PHE cc_start: 0.8322 (m-80) cc_final: 0.8030 (m-10) REVERT: H 140 ARG cc_start: 0.8964 (ttp-110) cc_final: 0.8589 (ttp-110) REVERT: I 39 ASN cc_start: 0.9248 (t0) cc_final: 0.8951 (t0) REVERT: I 44 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8278 (mtm-85) REVERT: I 51 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8714 (tm-30) REVERT: I 52 GLN cc_start: 0.9356 (mm-40) cc_final: 0.8853 (mm-40) REVERT: I 84 TYR cc_start: 0.8799 (m-80) cc_final: 0.8128 (m-80) REVERT: I 89 MET cc_start: 0.9628 (mtt) cc_final: 0.9184 (mtp) REVERT: I 110 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8396 (tt0) REVERT: I 134 PHE cc_start: 0.8673 (m-80) cc_final: 0.8159 (m-10) REVERT: I 144 LYS cc_start: 0.9130 (tppt) cc_final: 0.8832 (tppt) REVERT: I 159 ASP cc_start: 0.9654 (p0) cc_final: 0.9427 (p0) REVERT: I 162 PHE cc_start: 0.9537 (m-80) cc_final: 0.9155 (m-80) REVERT: J 21 ILE cc_start: 0.8958 (mt) cc_final: 0.8614 (mt) REVERT: J 39 ASN cc_start: 0.8748 (t0) cc_final: 0.8072 (t0) REVERT: J 43 MET cc_start: 0.9185 (mmm) cc_final: 0.8796 (mmm) REVERT: J 48 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8491 (tpp80) REVERT: J 53 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8207 (mm-30) REVERT: J 73 GLN cc_start: 0.8611 (pp30) cc_final: 0.8193 (pp30) REVERT: J 74 ILE cc_start: 0.9724 (mm) cc_final: 0.9332 (mm) REVERT: J 89 MET cc_start: 0.9349 (mtm) cc_final: 0.8726 (mtm) REVERT: J 99 TYR cc_start: 0.8788 (t80) cc_final: 0.8528 (t80) REVERT: J 134 PHE cc_start: 0.8541 (m-80) cc_final: 0.8215 (m-10) REVERT: J 140 ARG cc_start: 0.8910 (ttp-110) cc_final: 0.8501 (ttp-110) REVERT: J 144 LYS cc_start: 0.8948 (tppt) cc_final: 0.8694 (tppt) REVERT: J 158 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8655 (mt-10) REVERT: J 162 PHE cc_start: 0.9293 (m-80) cc_final: 0.9027 (m-80) REVERT: K 20 ARG cc_start: 0.9164 (mmm160) cc_final: 0.8729 (mmt180) REVERT: K 21 ILE cc_start: 0.9129 (mt) cc_final: 0.8802 (mt) REVERT: K 39 ASN cc_start: 0.9149 (t0) cc_final: 0.8638 (t0) REVERT: K 89 MET cc_start: 0.9622 (mtt) cc_final: 0.9136 (mtm) REVERT: K 110 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8320 (mt-10) REVERT: K 134 PHE cc_start: 0.8888 (m-80) cc_final: 0.8525 (m-10) REVERT: K 140 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8354 (ttp-110) REVERT: K 144 LYS cc_start: 0.9065 (tppt) cc_final: 0.8698 (tppt) REVERT: L 113 HIS cc_start: 0.9000 (m-70) cc_final: 0.8768 (m-70) REVERT: L 134 PHE cc_start: 0.8719 (m-80) cc_final: 0.8452 (m-10) REVERT: L 162 PHE cc_start: 0.9570 (m-80) cc_final: 0.9230 (m-80) REVERT: M 20 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8816 (mmt180) REVERT: M 36 ILE cc_start: 0.9678 (mm) cc_final: 0.9284 (mm) REVERT: M 39 ASN cc_start: 0.8863 (t0) cc_final: 0.8241 (t0) REVERT: M 43 MET cc_start: 0.9250 (mmm) cc_final: 0.9012 (mmm) REVERT: M 51 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8815 (tm-30) REVERT: M 52 GLN cc_start: 0.9406 (mm-40) cc_final: 0.8944 (mm-40) REVERT: M 77 LYS cc_start: 0.8575 (ttpt) cc_final: 0.7882 (tmmt) REVERT: M 158 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8730 (mt-10) REVERT: N 39 ASN cc_start: 0.9133 (t0) cc_final: 0.8694 (t0) REVERT: N 43 MET cc_start: 0.9272 (mmm) cc_final: 0.8859 (mmm) REVERT: N 78 TYR cc_start: 0.9075 (m-10) cc_final: 0.8828 (m-10) REVERT: N 89 MET cc_start: 0.9619 (mtt) cc_final: 0.9285 (mtp) REVERT: N 94 LYS cc_start: 0.9506 (tttt) cc_final: 0.9237 (ttmm) REVERT: N 110 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8957 (mt-10) REVERT: N 120 MET cc_start: 0.8726 (ppp) cc_final: 0.8486 (ppp) REVERT: N 134 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7531 (t80) REVERT: N 144 LYS cc_start: 0.9018 (tppt) cc_final: 0.8696 (tppt) REVERT: P 39 ASN cc_start: 0.8928 (t0) cc_final: 0.7373 (t0) REVERT: P 41 GLU cc_start: 0.8847 (pm20) cc_final: 0.8591 (pm20) REVERT: P 113 HIS cc_start: 0.9050 (m-70) cc_final: 0.8825 (m-70) REVERT: P 152 LYS cc_start: 0.9683 (ttpp) cc_final: 0.9220 (pttp) REVERT: R 39 ASN cc_start: 0.9014 (t0) cc_final: 0.8687 (t0) REVERT: R 48 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8800 (tpp80) REVERT: R 89 MET cc_start: 0.9240 (mtp) cc_final: 0.8741 (ptp) REVERT: R 113 HIS cc_start: 0.9081 (m-70) cc_final: 0.8783 (m-70) REVERT: R 140 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8329 (ttp-110) REVERT: R 144 LYS cc_start: 0.8826 (tptt) cc_final: 0.8626 (tppt) REVERT: T 89 MET cc_start: 0.9317 (mtm) cc_final: 0.8996 (mtm) REVERT: T 99 TYR cc_start: 0.9144 (t80) cc_final: 0.8880 (t80) REVERT: T 117 TRP cc_start: 0.8768 (t-100) cc_final: 0.8556 (t-100) REVERT: T 134 PHE cc_start: 0.8413 (m-80) cc_final: 0.8095 (m-10) REVERT: T 152 LYS cc_start: 0.9676 (ttpp) cc_final: 0.9150 (pttp) REVERT: T 162 PHE cc_start: 0.9310 (m-80) cc_final: 0.8982 (m-80) REVERT: a 38 GLN cc_start: 0.8951 (tp40) cc_final: 0.8542 (tm-30) REVERT: a 82 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9549 (tp) REVERT: a 127 LYS cc_start: 0.9469 (pttm) cc_final: 0.9164 (pttm) REVERT: a 202 ARG cc_start: 0.9162 (mtm-85) cc_final: 0.8705 (ptp-170) REVERT: b 87 ILE cc_start: 0.9629 (mt) cc_final: 0.9274 (tt) REVERT: b 113 MET cc_start: 0.8715 (tmm) cc_final: 0.8316 (tmm) REVERT: b 158 MET cc_start: 0.9082 (tpp) cc_final: 0.8777 (tpp) REVERT: b 170 MET cc_start: 0.8709 (mtm) cc_final: 0.7692 (mmm) REVERT: b 173 LYS cc_start: 0.8818 (pttt) cc_final: 0.8571 (ptpt) REVERT: b 187 PHE cc_start: 0.1821 (OUTLIER) cc_final: 0.1404 (m-80) REVERT: c 198 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8885 (pt0) REVERT: d 186 THR cc_start: 0.4930 (OUTLIER) cc_final: 0.3936 (m) REVERT: e 38 GLN cc_start: 0.9179 (tp40) cc_final: 0.8919 (tp-100) REVERT: e 59 MET cc_start: 0.9094 (mmm) cc_final: 0.8548 (mmm) REVERT: e 63 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9231 (mp) REVERT: e 113 MET cc_start: 0.8946 (tmm) cc_final: 0.8487 (tmm) REVERT: e 121 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8681 (tm-30) REVERT: e 125 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8749 (mm-40) REVERT: e 140 VAL cc_start: 0.8854 (t) cc_final: 0.8624 (p) REVERT: e 158 MET cc_start: 0.9228 (tpp) cc_final: 0.8824 (tpp) REVERT: f 39 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8191 (mm-40) REVERT: f 170 MET cc_start: 0.9045 (ptt) cc_final: 0.8795 (ptt) REVERT: f 171 LYS cc_start: 0.8823 (pttt) cc_final: 0.8588 (ptpp) REVERT: g 113 MET cc_start: 0.8891 (tpp) cc_final: 0.8660 (tpp) REVERT: g 158 MET cc_start: 0.9148 (tpp) cc_final: 0.8796 (tpp) REVERT: g 165 TYR cc_start: 0.8944 (m-80) cc_final: 0.8687 (m-80) REVERT: g 169 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8293 (pp) REVERT: g 195 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8946 (mmmm) REVERT: h 11 ASP cc_start: 0.7933 (m-30) cc_final: 0.7486 (m-30) REVERT: h 21 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9198 (mtmm) REVERT: h 158 MET cc_start: 0.8528 (tpp) cc_final: 0.8244 (tpp) REVERT: h 171 LYS cc_start: 0.8791 (pttm) cc_final: 0.8504 (pttt) REVERT: h 187 PHE cc_start: 0.0533 (OUTLIER) cc_final: 0.0066 (m-80) REVERT: i 39 GLN cc_start: 0.9115 (mm110) cc_final: 0.8884 (mm-40) REVERT: i 127 LYS cc_start: 0.9663 (pttp) cc_final: 0.9393 (ptpp) REVERT: i 158 MET cc_start: 0.9083 (tpp) cc_final: 0.8750 (tpp) REVERT: j 113 MET cc_start: 0.9020 (tpp) cc_final: 0.8571 (tpp) REVERT: j 126 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9224 (tp) REVERT: j 127 LYS cc_start: 0.9468 (pttp) cc_final: 0.9172 (pttp) REVERT: j 158 MET cc_start: 0.9058 (tpp) cc_final: 0.8685 (tpp) REVERT: j 199 ASP cc_start: 0.9260 (p0) cc_final: 0.9051 (p0) REVERT: k 158 MET cc_start: 0.8487 (tpp) cc_final: 0.8268 (tpp) REVERT: k 186 THR cc_start: 0.5805 (OUTLIER) cc_final: 0.5168 (m) REVERT: k 201 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8061 (mm-30) REVERT: l 113 MET cc_start: 0.9135 (tpp) cc_final: 0.8754 (tpp) REVERT: l 126 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9163 (tt) REVERT: l 135 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7720 (mp0) REVERT: m 82 LEU cc_start: 0.9815 (tp) cc_final: 0.9604 (tp) REVERT: m 96 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8742 (mt-10) REVERT: m 127 LYS cc_start: 0.9444 (pttp) cc_final: 0.9190 (pttp) REVERT: m 158 MET cc_start: 0.9030 (tpp) cc_final: 0.8611 (tpp) REVERT: m 198 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8695 (tm-30) REVERT: n 152 ASP cc_start: 0.9349 (m-30) cc_final: 0.9130 (m-30) REVERT: n 187 PHE cc_start: -0.0198 (OUTLIER) cc_final: -0.0568 (m-80) REVERT: n 202 ARG cc_start: 0.9096 (mtm-85) cc_final: 0.8772 (ptp-170) REVERT: p 38 GLN cc_start: 0.8970 (tp40) cc_final: 0.8678 (tp40) REVERT: p 82 LEU cc_start: 0.9744 (tp) cc_final: 0.9462 (tp) REVERT: p 187 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.5692 (t80) REVERT: r 38 GLN cc_start: 0.9096 (tp40) cc_final: 0.8767 (tp40) REVERT: r 39 GLN cc_start: 0.8878 (mm110) cc_final: 0.7994 (mm-40) REVERT: r 44 MET cc_start: 0.8936 (tpp) cc_final: 0.8660 (tpp) REVERT: r 135 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8228 (mp0) REVERT: r 158 MET cc_start: 0.8594 (tpp) cc_final: 0.8367 (tpp) REVERT: t 187 PHE cc_start: -0.0338 (OUTLIER) cc_final: -0.1065 (m-80) REVERT: t 199 ASP cc_start: 0.9365 (p0) cc_final: 0.9090 (p0) REVERT: t 202 ARG cc_start: 0.9015 (mtm-85) cc_final: 0.8466 (mtm-85) outliers start: 173 outliers final: 90 residues processed: 1464 average time/residue: 0.6045 time to fit residues: 1426.5959 Evaluate side-chains 1323 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1214 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 134 PHE Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 187 PHE Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 186 THR Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 186 THR Chi-restraints excluded: chain f residue 39 GLN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 169 LEU Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 187 PHE Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 148 VAL Chi-restraints excluded: chain i residue 176 THR Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 58 LYS Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 186 THR Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 188 SER Chi-restraints excluded: chain n residue 135 GLU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 187 PHE Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 186 THR Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 148 VAL Chi-restraints excluded: chain t residue 187 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 514 optimal weight: 40.0000 chunk 350 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 459 optimal weight: 40.0000 chunk 254 optimal weight: 9.9990 chunk 527 optimal weight: 20.0000 chunk 426 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 315 optimal weight: 9.9990 chunk 554 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 overall best weight: 9.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 ASN b 39 GLN b 43 ASN b 180 HIS d 38 GLN f 39 GLN f 57 ASN g 39 GLN g 43 ASN g 125 GLN g 144 HIS h 39 GLN h 125 GLN ** i 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 14 ASN j 39 GLN j 43 ASN j 57 ASN k 136 GLN l 39 GLN l 43 ASN p 39 GLN t 39 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 58327 Z= 0.310 Angle : 0.806 13.438 81125 Z= 0.447 Chirality : 0.043 0.167 9340 Planarity : 0.005 0.058 8642 Dihedral : 17.319 67.785 11967 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.60 % Allowed : 22.55 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5950 helix: 0.63 (0.08), residues: 4335 sheet: -0.09 (0.32), residues: 204 loop : -2.50 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 117 HIS 0.017 0.001 HIS i 180 PHE 0.020 0.002 PHE b 77 TYR 0.034 0.002 TYR R 17 ARG 0.013 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1477 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1297 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 52 GLN cc_start: 0.9343 (mm-40) cc_final: 0.8961 (mm-40) REVERT: A 89 MET cc_start: 0.9430 (mtm) cc_final: 0.9021 (mtm) REVERT: A 110 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8479 (mt-10) REVERT: A 120 MET cc_start: 0.8377 (ppp) cc_final: 0.8142 (ppp) REVERT: A 140 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.8074 (ttp-110) REVERT: A 162 PHE cc_start: 0.9582 (m-80) cc_final: 0.9187 (m-80) REVERT: B 39 ASN cc_start: 0.9233 (t0) cc_final: 0.8973 (t0) REVERT: B 51 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 52 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8271 (mm-40) REVERT: B 99 TYR cc_start: 0.9011 (t80) cc_final: 0.8705 (t80) REVERT: B 120 MET cc_start: 0.7562 (ppp) cc_final: 0.7162 (ppp) REVERT: B 158 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8512 (mt-10) REVERT: C 39 ASN cc_start: 0.8804 (t0) cc_final: 0.8399 (t0) REVERT: C 51 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 52 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8940 (mm-40) REVERT: C 89 MET cc_start: 0.9522 (mtm) cc_final: 0.9156 (mtm) REVERT: C 134 PHE cc_start: 0.8324 (m-80) cc_final: 0.7962 (m-10) REVERT: C 162 PHE cc_start: 0.9651 (m-80) cc_final: 0.9314 (m-80) REVERT: D 20 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8446 (mmt180) REVERT: D 39 ASN cc_start: 0.9345 (t0) cc_final: 0.8946 (t0) REVERT: D 89 MET cc_start: 0.9429 (mtp) cc_final: 0.9052 (mtp) REVERT: D 94 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.8860 (tptt) REVERT: D 134 PHE cc_start: 0.8387 (m-80) cc_final: 0.8046 (m-10) REVERT: D 158 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8860 (mt-10) REVERT: E 12 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8606 (t) REVERT: E 17 TYR cc_start: 0.9086 (t80) cc_final: 0.8692 (t80) REVERT: E 21 ILE cc_start: 0.9202 (mt) cc_final: 0.8862 (mt) REVERT: E 39 ASN cc_start: 0.8955 (t0) cc_final: 0.8340 (t0) REVERT: E 52 GLN cc_start: 0.9372 (mm-40) cc_final: 0.8914 (mm-40) REVERT: E 89 MET cc_start: 0.9531 (mtm) cc_final: 0.8898 (mtm) REVERT: E 152 LYS cc_start: 0.9699 (ttpp) cc_final: 0.9373 (ptmm) REVERT: E 162 PHE cc_start: 0.9616 (m-80) cc_final: 0.9393 (m-80) REVERT: F 27 THR cc_start: 0.8961 (m) cc_final: 0.8673 (m) REVERT: F 39 ASN cc_start: 0.9214 (t0) cc_final: 0.8898 (t0) REVERT: F 51 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8852 (tm-30) REVERT: F 52 GLN cc_start: 0.9485 (mm-40) cc_final: 0.8885 (mm-40) REVERT: F 55 TYR cc_start: 0.9128 (t80) cc_final: 0.8879 (t80) REVERT: F 134 PHE cc_start: 0.8651 (m-80) cc_final: 0.8312 (m-10) REVERT: F 162 PHE cc_start: 0.9478 (m-80) cc_final: 0.9196 (m-80) REVERT: G 27 THR cc_start: 0.9126 (m) cc_final: 0.8694 (p) REVERT: G 36 ILE cc_start: 0.9742 (mm) cc_final: 0.9462 (pt) REVERT: G 111 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9395 (tp) REVERT: G 162 PHE cc_start: 0.9413 (m-80) cc_final: 0.8846 (m-80) REVERT: G 163 LYS cc_start: 0.9391 (ptpp) cc_final: 0.9151 (ptpp) REVERT: H 43 MET cc_start: 0.9327 (mmm) cc_final: 0.9002 (mmm) REVERT: H 44 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8577 (mtm-85) REVERT: H 48 ARG cc_start: 0.8982 (ttm110) cc_final: 0.8675 (ttm-80) REVERT: H 89 MET cc_start: 0.9394 (mtt) cc_final: 0.8755 (mtm) REVERT: H 99 TYR cc_start: 0.9306 (t80) cc_final: 0.9036 (t80) REVERT: H 120 MET cc_start: 0.7478 (ppp) cc_final: 0.7046 (ppp) REVERT: H 134 PHE cc_start: 0.8348 (m-80) cc_final: 0.7920 (m-10) REVERT: H 140 ARG cc_start: 0.8937 (ttp-110) cc_final: 0.8613 (ttp-110) REVERT: H 144 LYS cc_start: 0.9262 (tppt) cc_final: 0.9001 (tppt) REVERT: I 39 ASN cc_start: 0.9275 (t0) cc_final: 0.8986 (t0) REVERT: I 51 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8849 (tm-30) REVERT: I 89 MET cc_start: 0.9690 (mtt) cc_final: 0.9255 (mtp) REVERT: I 110 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8387 (tt0) REVERT: I 134 PHE cc_start: 0.8646 (m-80) cc_final: 0.8222 (m-10) REVERT: I 144 LYS cc_start: 0.9097 (tppt) cc_final: 0.8789 (tppt) REVERT: I 158 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8691 (mt-10) REVERT: I 162 PHE cc_start: 0.9551 (m-80) cc_final: 0.9206 (m-80) REVERT: J 39 ASN cc_start: 0.8587 (t0) cc_final: 0.7360 (t0) REVERT: J 43 MET cc_start: 0.9258 (mmm) cc_final: 0.8916 (mmm) REVERT: J 48 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8389 (tpp80) REVERT: J 53 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8079 (mt-10) REVERT: J 73 GLN cc_start: 0.8717 (pp30) cc_final: 0.8279 (pp30) REVERT: J 74 ILE cc_start: 0.9741 (mm) cc_final: 0.9289 (mm) REVERT: J 89 MET cc_start: 0.9435 (mtm) cc_final: 0.8638 (mtm) REVERT: J 99 TYR cc_start: 0.8674 (t80) cc_final: 0.8356 (t80) REVERT: J 134 PHE cc_start: 0.8617 (m-80) cc_final: 0.8244 (m-10) REVERT: J 140 ARG cc_start: 0.8863 (ttp-110) cc_final: 0.8331 (ttp-110) REVERT: J 158 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8666 (mt-10) REVERT: K 20 ARG cc_start: 0.9149 (mmm160) cc_final: 0.8794 (mmt180) REVERT: K 21 ILE cc_start: 0.9238 (mt) cc_final: 0.8908 (mt) REVERT: K 39 ASN cc_start: 0.8979 (t0) cc_final: 0.8643 (t0) REVERT: K 73 GLN cc_start: 0.8521 (pp30) cc_final: 0.8110 (pp30) REVERT: K 74 ILE cc_start: 0.9649 (mm) cc_final: 0.9222 (mm) REVERT: K 89 MET cc_start: 0.9644 (mtt) cc_final: 0.9143 (mtm) REVERT: K 110 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8514 (mt-10) REVERT: K 134 PHE cc_start: 0.8858 (m-80) cc_final: 0.8394 (m-10) REVERT: K 140 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8290 (ttp-110) REVERT: K 144 LYS cc_start: 0.9160 (tppt) cc_final: 0.8709 (tppt) REVERT: L 48 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8046 (ttm-80) REVERT: L 113 HIS cc_start: 0.9012 (m-70) cc_final: 0.8800 (m-70) REVERT: L 134 PHE cc_start: 0.8802 (m-80) cc_final: 0.8423 (m-10) REVERT: L 152 LYS cc_start: 0.9697 (ttpp) cc_final: 0.9136 (pttp) REVERT: L 156 GLU cc_start: 0.9381 (pt0) cc_final: 0.9138 (pp20) REVERT: L 162 PHE cc_start: 0.9563 (m-80) cc_final: 0.9230 (m-80) REVERT: M 20 ARG cc_start: 0.9226 (mmm160) cc_final: 0.8874 (mmt180) REVERT: M 36 ILE cc_start: 0.9749 (mm) cc_final: 0.9400 (mm) REVERT: M 39 ASN cc_start: 0.8806 (t0) cc_final: 0.8391 (t0) REVERT: M 43 MET cc_start: 0.9266 (mmm) cc_final: 0.9043 (mmm) REVERT: M 51 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8831 (tm-30) REVERT: M 52 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8866 (mm-40) REVERT: M 73 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8965 (tm-30) REVERT: N 39 ASN cc_start: 0.9162 (t0) cc_final: 0.8899 (t0) REVERT: N 48 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8450 (ttm110) REVERT: N 89 MET cc_start: 0.9649 (mtt) cc_final: 0.9274 (mtp) REVERT: N 120 MET cc_start: 0.8716 (ppp) cc_final: 0.8470 (ppp) REVERT: N 134 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7596 (t80) REVERT: P 39 ASN cc_start: 0.8979 (t0) cc_final: 0.7207 (t0) REVERT: P 51 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8620 (tm-30) REVERT: P 110 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: P 152 LYS cc_start: 0.9708 (ttpp) cc_final: 0.9238 (pttp) REVERT: P 162 PHE cc_start: 0.9513 (m-80) cc_final: 0.9270 (m-80) REVERT: R 48 ARG cc_start: 0.9024 (tpp80) cc_final: 0.8772 (tpp80) REVERT: R 113 HIS cc_start: 0.9001 (m-70) cc_final: 0.8722 (m-70) REVERT: R 140 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8325 (ttp-110) REVERT: T 89 MET cc_start: 0.9379 (mtm) cc_final: 0.8809 (mtm) REVERT: T 99 TYR cc_start: 0.9161 (t80) cc_final: 0.8881 (t80) REVERT: T 134 PHE cc_start: 0.8375 (m-80) cc_final: 0.8029 (m-10) REVERT: T 162 PHE cc_start: 0.9319 (m-80) cc_final: 0.9009 (m-80) REVERT: a 38 GLN cc_start: 0.9005 (tp40) cc_final: 0.8610 (tp40) REVERT: a 191 GLU cc_start: 0.9094 (pm20) cc_final: 0.8796 (pm20) REVERT: b 39 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: b 113 MET cc_start: 0.8773 (tmm) cc_final: 0.8319 (tmm) REVERT: b 158 MET cc_start: 0.9116 (tpp) cc_final: 0.8815 (tpp) REVERT: b 170 MET cc_start: 0.8646 (mtm) cc_final: 0.7615 (mmm) REVERT: b 173 LYS cc_start: 0.8824 (pttt) cc_final: 0.8587 (ptpt) REVERT: c 191 GLU cc_start: 0.8629 (pm20) cc_final: 0.8412 (pm20) REVERT: d 59 MET cc_start: 0.9034 (mmp) cc_final: 0.8804 (mmm) REVERT: d 113 MET cc_start: 0.9077 (tpp) cc_final: 0.8524 (tpp) REVERT: d 126 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9362 (tp) REVERT: d 152 ASP cc_start: 0.9491 (m-30) cc_final: 0.9197 (m-30) REVERT: e 27 ILE cc_start: 0.9623 (mm) cc_final: 0.9330 (tp) REVERT: e 59 MET cc_start: 0.9176 (mmm) cc_final: 0.8669 (mmm) REVERT: e 63 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9245 (mp) REVERT: e 113 MET cc_start: 0.8961 (tmm) cc_final: 0.8515 (tmm) REVERT: e 121 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8709 (tm-30) REVERT: e 125 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8712 (mp10) REVERT: e 158 MET cc_start: 0.9378 (tpp) cc_final: 0.8953 (tpp) REVERT: f 44 MET cc_start: 0.9032 (ttm) cc_final: 0.8790 (ttm) REVERT: g 11 ASP cc_start: 0.8461 (m-30) cc_final: 0.8149 (m-30) REVERT: g 39 GLN cc_start: 0.9209 (mm110) cc_final: 0.8676 (mm-40) REVERT: g 113 MET cc_start: 0.9050 (tpp) cc_final: 0.8849 (tpp) REVERT: g 158 MET cc_start: 0.9199 (tpp) cc_final: 0.8853 (tpp) REVERT: g 169 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (pp) REVERT: g 171 LYS cc_start: 0.9319 (mtmm) cc_final: 0.9081 (tptp) REVERT: h 11 ASP cc_start: 0.8208 (m-30) cc_final: 0.7907 (m-30) REVERT: h 158 MET cc_start: 0.8928 (tpp) cc_final: 0.8633 (tpp) REVERT: h 171 LYS cc_start: 0.8673 (pttm) cc_final: 0.8413 (pttm) REVERT: i 39 GLN cc_start: 0.9233 (mm110) cc_final: 0.9006 (mm-40) REVERT: i 127 LYS cc_start: 0.9698 (pttp) cc_final: 0.9453 (ptpp) REVERT: i 158 MET cc_start: 0.9172 (tpp) cc_final: 0.8739 (tpp) REVERT: i 201 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8221 (mm-30) REVERT: j 32 MET cc_start: 0.9121 (mmp) cc_final: 0.8888 (mmp) REVERT: j 113 MET cc_start: 0.9127 (tpp) cc_final: 0.8688 (tpp) REVERT: j 126 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9210 (tp) REVERT: j 127 LYS cc_start: 0.9442 (pttp) cc_final: 0.9163 (pttp) REVERT: j 158 MET cc_start: 0.9256 (tpp) cc_final: 0.8970 (tpp) REVERT: k 158 MET cc_start: 0.8836 (tpp) cc_final: 0.8607 (tpp) REVERT: k 195 LYS cc_start: 0.9278 (mttm) cc_final: 0.8917 (mppt) REVERT: k 199 ASP cc_start: 0.9284 (p0) cc_final: 0.8686 (p0) REVERT: l 39 GLN cc_start: 0.9058 (mm110) cc_final: 0.7945 (mm-40) REVERT: l 113 MET cc_start: 0.9160 (tpp) cc_final: 0.8823 (tpp) REVERT: l 126 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9091 (tt) REVERT: l 135 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7682 (mp0) REVERT: l 191 GLU cc_start: 0.8402 (pm20) cc_final: 0.8169 (pm20) REVERT: m 96 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8663 (mt-10) REVERT: m 127 LYS cc_start: 0.9577 (pttp) cc_final: 0.9297 (pttp) REVERT: m 158 MET cc_start: 0.9088 (tpp) cc_final: 0.8644 (tpp) REVERT: m 170 MET cc_start: 0.9346 (mtm) cc_final: 0.8574 (mmm) REVERT: m 195 LYS cc_start: 0.9470 (tppp) cc_final: 0.9228 (tppt) REVERT: m 198 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8264 (tm-30) REVERT: m 199 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8613 (p0) REVERT: n 44 MET cc_start: 0.9039 (mmm) cc_final: 0.8803 (mmm) REVERT: p 38 GLN cc_start: 0.9119 (tp40) cc_final: 0.8895 (tp40) REVERT: p 39 GLN cc_start: 0.8938 (mm110) cc_final: 0.8711 (mm-40) REVERT: p 187 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.5899 (t80) REVERT: r 158 MET cc_start: 0.8752 (tpp) cc_final: 0.8510 (tpp) REVERT: r 171 LYS cc_start: 0.9208 (pttt) cc_final: 0.8929 (ptpp) REVERT: r 187 PHE cc_start: -0.1136 (OUTLIER) cc_final: -0.1819 (m-80) REVERT: t 21 LYS cc_start: 0.9520 (mttt) cc_final: 0.8917 (tmtt) REVERT: t 39 GLN cc_start: 0.8858 (mm110) cc_final: 0.8142 (mm-40) REVERT: t 194 TYR cc_start: 0.9153 (m-80) cc_final: 0.8801 (m-80) outliers start: 180 outliers final: 119 residues processed: 1397 average time/residue: 0.6260 time to fit residues: 1405.0052 Evaluate side-chains 1261 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1128 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 ASN Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 134 PHE Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 188 SER Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 39 GLN Chi-restraints excluded: chain b residue 69 LYS Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 35 LYS Chi-restraints excluded: chain d residue 38 GLN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 186 THR Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 125 GLN Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 169 LEU Chi-restraints excluded: chain g residue 180 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 163 ASN Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 176 THR Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 186 THR Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 153 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 188 SER Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain n residue 135 GLU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 170 MET Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 28 PHE Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 186 THR Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 97 THR Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain r residue 169 LEU Chi-restraints excluded: chain r residue 187 PHE Chi-restraints excluded: chain t residue 129 LEU Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 207 optimal weight: 9.9990 chunk 556 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 362 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 618 optimal weight: 7.9990 chunk 513 optimal weight: 10.0000 chunk 286 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 HIS L 73 GLN N 73 GLN b 43 ASN d 39 GLN d 125 GLN f 39 GLN g 43 ASN ** g 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 14 ASN ** k 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 ASN n 144 HIS r 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 58327 Z= 0.256 Angle : 0.814 12.897 81125 Z= 0.448 Chirality : 0.043 0.192 9340 Planarity : 0.005 0.068 8642 Dihedral : 17.259 83.675 11967 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.68 % Allowed : 23.47 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5950 helix: 0.60 (0.08), residues: 4335 sheet: 0.09 (0.33), residues: 204 loop : -2.49 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 117 HIS 0.012 0.001 HIS h 180 PHE 0.019 0.002 PHE b 77 TYR 0.028 0.002 TYR G 17 ARG 0.016 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1303 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 52 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8974 (mm-40) REVERT: A 89 MET cc_start: 0.9403 (mtm) cc_final: 0.8891 (mtm) REVERT: A 140 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8116 (ttp-110) REVERT: A 158 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 162 PHE cc_start: 0.9572 (m-80) cc_final: 0.9151 (m-80) REVERT: B 39 ASN cc_start: 0.9158 (t0) cc_final: 0.8821 (t0) REVERT: B 51 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8046 (tm-30) REVERT: B 52 GLN cc_start: 0.9263 (mm-40) cc_final: 0.7878 (mm-40) REVERT: B 84 TYR cc_start: 0.8792 (m-80) cc_final: 0.8358 (m-80) REVERT: B 99 TYR cc_start: 0.8900 (t80) cc_final: 0.7368 (t80) REVERT: B 108 LEU cc_start: 0.9410 (pt) cc_final: 0.9172 (mt) REVERT: B 120 MET cc_start: 0.7522 (ppp) cc_final: 0.7292 (ppp) REVERT: B 158 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8500 (mt-10) REVERT: C 39 ASN cc_start: 0.8796 (t0) cc_final: 0.8384 (t0) REVERT: C 51 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 52 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8765 (mm-40) REVERT: C 89 MET cc_start: 0.9493 (mtm) cc_final: 0.9092 (mtm) REVERT: C 134 PHE cc_start: 0.8338 (m-80) cc_final: 0.7953 (m-10) REVERT: D 20 ARG cc_start: 0.8878 (mmm160) cc_final: 0.8446 (mmt180) REVERT: D 39 ASN cc_start: 0.9231 (t0) cc_final: 0.8897 (t0) REVERT: D 89 MET cc_start: 0.9385 (mtp) cc_final: 0.9073 (mtp) REVERT: D 94 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.8854 (tptt) REVERT: D 134 PHE cc_start: 0.8298 (m-80) cc_final: 0.7971 (m-10) REVERT: D 158 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8879 (mt-10) REVERT: E 17 TYR cc_start: 0.8991 (t80) cc_final: 0.8609 (t80) REVERT: E 21 ILE cc_start: 0.9117 (mt) cc_final: 0.8777 (mt) REVERT: E 39 ASN cc_start: 0.8864 (t0) cc_final: 0.8293 (t0) REVERT: E 89 MET cc_start: 0.9517 (mtm) cc_final: 0.8927 (mtm) REVERT: E 162 PHE cc_start: 0.9614 (m-80) cc_final: 0.9361 (m-80) REVERT: F 27 THR cc_start: 0.8889 (m) cc_final: 0.8599 (m) REVERT: F 39 ASN cc_start: 0.9186 (t0) cc_final: 0.8840 (t0) REVERT: F 48 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8450 (ttm110) REVERT: F 51 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8825 (tm-30) REVERT: F 52 GLN cc_start: 0.9479 (mm-40) cc_final: 0.8900 (mm-40) REVERT: F 55 TYR cc_start: 0.9123 (t80) cc_final: 0.8876 (t80) REVERT: F 134 PHE cc_start: 0.8588 (m-80) cc_final: 0.8229 (m-10) REVERT: F 162 PHE cc_start: 0.9458 (m-80) cc_final: 0.9179 (m-80) REVERT: G 27 THR cc_start: 0.9008 (m) cc_final: 0.8546 (p) REVERT: G 36 ILE cc_start: 0.9703 (mm) cc_final: 0.9399 (pt) REVERT: G 96 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9559 (pp) REVERT: G 162 PHE cc_start: 0.9531 (m-80) cc_final: 0.8994 (m-80) REVERT: H 43 MET cc_start: 0.9363 (mmm) cc_final: 0.9067 (mmm) REVERT: H 48 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8605 (ttm-80) REVERT: H 89 MET cc_start: 0.9367 (mtt) cc_final: 0.8765 (mtm) REVERT: H 113 HIS cc_start: 0.9202 (m90) cc_final: 0.8751 (m90) REVERT: H 120 MET cc_start: 0.7514 (ppp) cc_final: 0.7069 (ppp) REVERT: H 134 PHE cc_start: 0.8332 (m-80) cc_final: 0.7953 (m-10) REVERT: H 140 ARG cc_start: 0.8933 (ttp-110) cc_final: 0.8630 (ttp-110) REVERT: H 152 LYS cc_start: 0.9747 (ttpp) cc_final: 0.9422 (pttp) REVERT: H 162 PHE cc_start: 0.9565 (m-80) cc_final: 0.9345 (m-80) REVERT: I 39 ASN cc_start: 0.9224 (t0) cc_final: 0.8920 (t0) REVERT: I 51 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8870 (tm-30) REVERT: I 89 MET cc_start: 0.9673 (mtt) cc_final: 0.9301 (mtp) REVERT: I 110 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8500 (tt0) REVERT: I 134 PHE cc_start: 0.8722 (m-80) cc_final: 0.8259 (m-10) REVERT: I 144 LYS cc_start: 0.9090 (tppt) cc_final: 0.8788 (tppt) REVERT: I 162 PHE cc_start: 0.9570 (m-80) cc_final: 0.9171 (m-80) REVERT: J 39 ASN cc_start: 0.8584 (t0) cc_final: 0.8279 (t0) REVERT: J 43 MET cc_start: 0.9228 (mmm) cc_final: 0.8896 (mmm) REVERT: J 48 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8359 (tpp80) REVERT: J 53 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7944 (mt-10) REVERT: J 73 GLN cc_start: 0.8716 (pp30) cc_final: 0.8305 (pp30) REVERT: J 74 ILE cc_start: 0.9738 (mm) cc_final: 0.9321 (mm) REVERT: J 89 MET cc_start: 0.9382 (mtm) cc_final: 0.8677 (mtm) REVERT: J 134 PHE cc_start: 0.8598 (m-80) cc_final: 0.8239 (m-10) REVERT: J 140 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8360 (ttp-110) REVERT: J 158 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8684 (mt-10) REVERT: K 20 ARG cc_start: 0.9092 (mmm160) cc_final: 0.8741 (mmt180) REVERT: K 21 ILE cc_start: 0.9167 (mt) cc_final: 0.8823 (mt) REVERT: K 39 ASN cc_start: 0.9041 (t0) cc_final: 0.8510 (t0) REVERT: K 44 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8389 (ptp-170) REVERT: K 73 GLN cc_start: 0.8668 (pp30) cc_final: 0.8229 (pp30) REVERT: K 74 ILE cc_start: 0.9688 (mm) cc_final: 0.9220 (mm) REVERT: K 77 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8335 (ttpp) REVERT: K 89 MET cc_start: 0.9625 (mtt) cc_final: 0.9140 (mtm) REVERT: K 110 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8504 (mt-10) REVERT: K 140 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8468 (ttp-110) REVERT: K 144 LYS cc_start: 0.9183 (tppt) cc_final: 0.8732 (tppt) REVERT: L 48 ARG cc_start: 0.8618 (ttm-80) cc_final: 0.7981 (ttm-80) REVERT: L 113 HIS cc_start: 0.9012 (m-70) cc_final: 0.8787 (m-70) REVERT: L 134 PHE cc_start: 0.8766 (m-80) cc_final: 0.8437 (m-10) REVERT: L 156 GLU cc_start: 0.9458 (pt0) cc_final: 0.9182 (pt0) REVERT: L 162 PHE cc_start: 0.9539 (m-80) cc_final: 0.9176 (m-80) REVERT: M 20 ARG cc_start: 0.9205 (mmm160) cc_final: 0.8856 (mmt180) REVERT: M 36 ILE cc_start: 0.9740 (mm) cc_final: 0.9389 (mm) REVERT: M 39 ASN cc_start: 0.8726 (t0) cc_final: 0.8432 (t0) REVERT: M 43 MET cc_start: 0.9266 (mmm) cc_final: 0.8999 (mmm) REVERT: M 44 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8155 (ptt-90) REVERT: M 51 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8826 (tm-30) REVERT: M 52 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8904 (mm-40) REVERT: M 73 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8937 (tm-30) REVERT: M 77 LYS cc_start: 0.9263 (ttpp) cc_final: 0.8925 (ptmm) REVERT: M 110 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8579 (mt-10) REVERT: N 39 ASN cc_start: 0.9066 (t0) cc_final: 0.8471 (t0) REVERT: N 43 MET cc_start: 0.9221 (mmm) cc_final: 0.8835 (mmm) REVERT: N 48 ARG cc_start: 0.8929 (ttm-80) cc_final: 0.8308 (ttm110) REVERT: N 89 MET cc_start: 0.9631 (mtt) cc_final: 0.9267 (mtp) REVERT: N 134 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7653 (t80) REVERT: P 43 MET cc_start: 0.8793 (mmm) cc_final: 0.8381 (mmm) REVERT: P 48 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8466 (tpp80) REVERT: P 89 MET cc_start: 0.9408 (mtm) cc_final: 0.8387 (ttm) REVERT: P 113 HIS cc_start: 0.9015 (m-70) cc_final: 0.8794 (m-70) REVERT: P 120 MET cc_start: 0.6876 (ppp) cc_final: 0.6510 (ppp) REVERT: P 162 PHE cc_start: 0.9434 (m-80) cc_final: 0.9223 (m-80) REVERT: R 48 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8704 (tpp80) REVERT: R 113 HIS cc_start: 0.9087 (m-70) cc_final: 0.8834 (m-70) REVERT: T 99 TYR cc_start: 0.9148 (t80) cc_final: 0.8155 (t80) REVERT: T 134 PHE cc_start: 0.8387 (m-80) cc_final: 0.8117 (m-10) REVERT: T 162 PHE cc_start: 0.9289 (m-80) cc_final: 0.8929 (m-80) REVERT: a 38 GLN cc_start: 0.8912 (tp40) cc_final: 0.7722 (tp40) REVERT: a 82 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9557 (tp) REVERT: b 32 MET cc_start: 0.8746 (mmp) cc_final: 0.8521 (mmp) REVERT: b 100 PHE cc_start: 0.8202 (m-80) cc_final: 0.7638 (m-80) REVERT: b 113 MET cc_start: 0.8835 (tmm) cc_final: 0.8394 (tmm) REVERT: b 158 MET cc_start: 0.9209 (tpp) cc_final: 0.8894 (tpp) REVERT: b 170 MET cc_start: 0.8569 (mtm) cc_final: 0.7465 (mmm) REVERT: b 173 LYS cc_start: 0.8849 (pttt) cc_final: 0.8591 (ptpt) REVERT: c 59 MET cc_start: 0.9332 (mmm) cc_final: 0.8990 (mmp) REVERT: d 113 MET cc_start: 0.9116 (tpp) cc_final: 0.8622 (tpp) REVERT: d 126 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9294 (tp) REVERT: d 152 ASP cc_start: 0.9477 (m-30) cc_final: 0.9183 (m-30) REVERT: d 171 LYS cc_start: 0.8949 (mttt) cc_final: 0.8727 (mttt) REVERT: e 24 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9458 (mm) REVERT: e 27 ILE cc_start: 0.9599 (mm) cc_final: 0.9337 (tp) REVERT: e 38 GLN cc_start: 0.9188 (tp40) cc_final: 0.8907 (tp-100) REVERT: e 39 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8611 (mm-40) REVERT: e 59 MET cc_start: 0.9202 (mmm) cc_final: 0.8899 (mmm) REVERT: e 63 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9211 (mp) REVERT: e 113 MET cc_start: 0.8966 (tmm) cc_final: 0.8515 (tmm) REVERT: e 121 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8613 (tm-30) REVERT: e 125 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8510 (mm-40) REVERT: e 158 MET cc_start: 0.9425 (tpp) cc_final: 0.9022 (tpp) REVERT: f 39 GLN cc_start: 0.9085 (mm110) cc_final: 0.8541 (mm-40) REVERT: f 121 GLU cc_start: 0.9265 (mp0) cc_final: 0.8946 (mp0) REVERT: f 170 MET cc_start: 0.9022 (ptt) cc_final: 0.8732 (ptt) REVERT: f 202 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8748 (ttm110) REVERT: g 11 ASP cc_start: 0.8444 (m-30) cc_final: 0.8107 (m-30) REVERT: g 158 MET cc_start: 0.9182 (tpp) cc_final: 0.8843 (tpp) REVERT: g 169 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8158 (pp) REVERT: g 171 LYS cc_start: 0.9346 (mtmm) cc_final: 0.9071 (tptp) REVERT: h 11 ASP cc_start: 0.8154 (m-30) cc_final: 0.7856 (m-30) REVERT: h 158 MET cc_start: 0.8949 (tpp) cc_final: 0.8592 (tpp) REVERT: h 171 LYS cc_start: 0.8726 (pttm) cc_final: 0.8458 (pttt) REVERT: h 195 LYS cc_start: 0.9303 (mptt) cc_final: 0.9059 (mppt) REVERT: h 199 ASP cc_start: 0.9178 (p0) cc_final: 0.8837 (p0) REVERT: h 202 ARG cc_start: 0.9163 (ptt-90) cc_final: 0.8251 (ptt-90) REVERT: i 39 GLN cc_start: 0.9226 (mm110) cc_final: 0.9020 (mm-40) REVERT: i 127 LYS cc_start: 0.9680 (pttp) cc_final: 0.9390 (ptpp) REVERT: i 158 MET cc_start: 0.9211 (tpp) cc_final: 0.8865 (tpp) REVERT: j 32 MET cc_start: 0.9074 (mmp) cc_final: 0.8735 (mmp) REVERT: j 82 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9370 (tp) REVERT: j 113 MET cc_start: 0.9147 (tpp) cc_final: 0.8711 (tpp) REVERT: j 126 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9243 (tp) REVERT: j 158 MET cc_start: 0.9193 (tpp) cc_final: 0.8943 (tpp) REVERT: k 32 MET cc_start: 0.9012 (mmp) cc_final: 0.8810 (mmp) REVERT: k 158 MET cc_start: 0.8859 (tpp) cc_final: 0.8612 (tpp) REVERT: k 199 ASP cc_start: 0.9300 (p0) cc_final: 0.8950 (p0) REVERT: l 96 GLU cc_start: 0.8803 (mp0) cc_final: 0.8389 (mp0) REVERT: l 113 MET cc_start: 0.9132 (tpp) cc_final: 0.8807 (tpp) REVERT: l 125 GLN cc_start: 0.9399 (mm-40) cc_final: 0.9159 (mm-40) REVERT: l 126 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9023 (tt) REVERT: l 135 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7698 (mp0) REVERT: l 191 GLU cc_start: 0.8315 (pm20) cc_final: 0.8110 (pm20) REVERT: m 96 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8621 (mt-10) REVERT: m 127 LYS cc_start: 0.9615 (pttp) cc_final: 0.9396 (pttp) REVERT: m 158 MET cc_start: 0.9016 (tpp) cc_final: 0.8613 (tpp) REVERT: m 170 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8315 (mmm) REVERT: m 195 LYS cc_start: 0.9525 (tppp) cc_final: 0.9309 (tppt) REVERT: m 198 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8866 (tm-30) REVERT: n 27 ILE cc_start: 0.9413 (mm) cc_final: 0.9152 (mt) REVERT: n 44 MET cc_start: 0.8790 (mmm) cc_final: 0.8503 (mmm) REVERT: n 113 MET cc_start: 0.8938 (tpp) cc_final: 0.8638 (tpp) REVERT: n 127 LYS cc_start: 0.9452 (ptpp) cc_final: 0.9224 (ptpp) REVERT: n 170 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: n 171 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8689 (tppt) REVERT: n 199 ASP cc_start: 0.9110 (p0) cc_final: 0.8900 (p0) REVERT: p 11 ASP cc_start: 0.8688 (m-30) cc_final: 0.8092 (m-30) REVERT: p 38 GLN cc_start: 0.9170 (tp40) cc_final: 0.8371 (tp40) REVERT: p 39 GLN cc_start: 0.9011 (mm110) cc_final: 0.8066 (mm-40) REVERT: p 125 GLN cc_start: 0.9161 (mp10) cc_final: 0.8899 (mp10) REVERT: p 127 LYS cc_start: 0.9500 (pttp) cc_final: 0.9237 (pttm) REVERT: p 187 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.5929 (t80) REVERT: r 42 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7139 (pt0) REVERT: r 44 MET cc_start: 0.8896 (tpp) cc_final: 0.8636 (tpt) REVERT: r 127 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.9429 (ptpp) REVERT: r 158 MET cc_start: 0.8650 (tpp) cc_final: 0.8392 (tpp) REVERT: r 171 LYS cc_start: 0.9156 (pttt) cc_final: 0.8917 (ptpp) REVERT: r 199 ASP cc_start: 0.9352 (p0) cc_final: 0.9019 (p0) REVERT: t 21 LYS cc_start: 0.9506 (mttt) cc_final: 0.8852 (tmtt) REVERT: t 127 LYS cc_start: 0.9424 (pttm) cc_final: 0.9168 (ptpp) outliers start: 184 outliers final: 113 residues processed: 1405 average time/residue: 0.5994 time to fit residues: 1355.7918 Evaluate side-chains 1287 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1159 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 134 PHE Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain f residue 58 LYS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 169 LEU Chi-restraints excluded: chain g residue 180 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 163 ASN Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 58 LYS Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 180 HIS Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain l residue 137 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 153 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 170 MET Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 200 ILE Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 170 MET Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 186 THR Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 97 THR Chi-restraints excluded: chain r residue 127 LYS Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain t residue 130 VAL Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 148 VAL Chi-restraints excluded: chain t residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 596 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 451 optimal weight: 20.0000 chunk 349 optimal weight: 7.9990 chunk 520 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 chunk 615 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 chunk 284 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 GLN b 39 GLN b 43 ASN b 180 HIS d 38 GLN e 43 ASN g 43 ASN k 144 HIS l 39 GLN l 94 HIS l 136 GLN r 39 GLN ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 58327 Z= 0.282 Angle : 0.846 15.246 81125 Z= 0.464 Chirality : 0.044 0.197 9340 Planarity : 0.005 0.057 8642 Dihedral : 17.288 84.072 11967 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.64 % Allowed : 25.33 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 5950 helix: 0.48 (0.08), residues: 4335 sheet: 0.12 (0.33), residues: 204 loop : -2.57 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 117 HIS 0.008 0.001 HIS h 180 PHE 0.019 0.002 PHE b 77 TYR 0.025 0.002 TYR A 99 ARG 0.014 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1260 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 52 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8984 (mm-40) REVERT: A 89 MET cc_start: 0.9433 (mtm) cc_final: 0.8747 (mtp) REVERT: A 110 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8576 (pt0) REVERT: A 140 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8128 (ttp-110) REVERT: A 158 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8724 (mt-10) REVERT: A 162 PHE cc_start: 0.9565 (m-80) cc_final: 0.9158 (m-80) REVERT: B 39 ASN cc_start: 0.9242 (t0) cc_final: 0.8941 (t0) REVERT: B 51 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 52 GLN cc_start: 0.9280 (mm-40) cc_final: 0.7962 (mm-40) REVERT: B 84 TYR cc_start: 0.8823 (m-80) cc_final: 0.8415 (m-80) REVERT: B 99 TYR cc_start: 0.8907 (t80) cc_final: 0.7445 (t80) REVERT: B 108 LEU cc_start: 0.9448 (pt) cc_final: 0.9233 (mt) REVERT: B 120 MET cc_start: 0.7778 (ppp) cc_final: 0.7558 (ppp) REVERT: B 134 PHE cc_start: 0.8105 (m-80) cc_final: 0.7745 (m-80) REVERT: C 39 ASN cc_start: 0.8809 (t0) cc_final: 0.8476 (t0) REVERT: C 51 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8644 (tm-30) REVERT: C 52 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8888 (mm-40) REVERT: C 89 MET cc_start: 0.9426 (mtm) cc_final: 0.9072 (mtm) REVERT: C 134 PHE cc_start: 0.8279 (m-80) cc_final: 0.7992 (m-80) REVERT: D 20 ARG cc_start: 0.8889 (mmm160) cc_final: 0.8300 (mmt180) REVERT: D 39 ASN cc_start: 0.9177 (t0) cc_final: 0.8513 (t0) REVERT: D 89 MET cc_start: 0.9386 (mtp) cc_final: 0.9032 (mtp) REVERT: D 94 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.8844 (tppt) REVERT: D 134 PHE cc_start: 0.8301 (m-80) cc_final: 0.8037 (m-10) REVERT: E 17 TYR cc_start: 0.9004 (t80) cc_final: 0.8642 (t80) REVERT: E 21 ILE cc_start: 0.9145 (mt) cc_final: 0.8799 (mt) REVERT: E 39 ASN cc_start: 0.8787 (t0) cc_final: 0.7462 (t0) REVERT: E 89 MET cc_start: 0.9507 (mtm) cc_final: 0.8938 (mtm) REVERT: E 162 PHE cc_start: 0.9553 (m-80) cc_final: 0.9327 (m-80) REVERT: F 27 THR cc_start: 0.8936 (m) cc_final: 0.8634 (m) REVERT: F 39 ASN cc_start: 0.9195 (t0) cc_final: 0.8846 (t0) REVERT: F 48 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8423 (ttm110) REVERT: F 51 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8838 (tm-30) REVERT: F 52 GLN cc_start: 0.9494 (mm-40) cc_final: 0.8920 (mm-40) REVERT: F 55 TYR cc_start: 0.9139 (t80) cc_final: 0.8882 (t80) REVERT: F 134 PHE cc_start: 0.8529 (m-80) cc_final: 0.8175 (m-10) REVERT: F 144 LYS cc_start: 0.9063 (tppt) cc_final: 0.8792 (tppt) REVERT: F 162 PHE cc_start: 0.9454 (m-80) cc_final: 0.9161 (m-80) REVERT: G 27 THR cc_start: 0.9060 (m) cc_final: 0.8613 (p) REVERT: G 36 ILE cc_start: 0.9705 (mm) cc_final: 0.9462 (pt) REVERT: G 96 LEU cc_start: 0.9789 (OUTLIER) cc_final: 0.9565 (pp) REVERT: G 111 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9325 (tp) REVERT: G 162 PHE cc_start: 0.9470 (m-80) cc_final: 0.9051 (m-80) REVERT: H 43 MET cc_start: 0.9375 (mmm) cc_final: 0.9047 (mmm) REVERT: H 89 MET cc_start: 0.9377 (mtt) cc_final: 0.8817 (mtm) REVERT: H 113 HIS cc_start: 0.9215 (m90) cc_final: 0.8761 (m90) REVERT: H 120 MET cc_start: 0.7631 (ppp) cc_final: 0.7167 (ppp) REVERT: H 134 PHE cc_start: 0.8390 (m-80) cc_final: 0.7962 (m-10) REVERT: H 140 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8507 (ttp-110) REVERT: H 152 LYS cc_start: 0.9749 (ttpp) cc_final: 0.9443 (pttp) REVERT: I 39 ASN cc_start: 0.9216 (t0) cc_final: 0.8896 (t0) REVERT: I 51 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8897 (tm-30) REVERT: I 89 MET cc_start: 0.9653 (mtt) cc_final: 0.9264 (mtp) REVERT: I 110 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8381 (tt0) REVERT: I 134 PHE cc_start: 0.8648 (m-80) cc_final: 0.8289 (m-10) REVERT: I 144 LYS cc_start: 0.8928 (tppt) cc_final: 0.8615 (tppt) REVERT: I 162 PHE cc_start: 0.9568 (m-80) cc_final: 0.9197 (m-80) REVERT: J 39 ASN cc_start: 0.8609 (t0) cc_final: 0.8054 (t0) REVERT: J 43 MET cc_start: 0.9180 (mmm) cc_final: 0.8759 (mmm) REVERT: J 48 ARG cc_start: 0.8698 (ttm110) cc_final: 0.8306 (tpp80) REVERT: J 53 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7891 (mt-10) REVERT: J 99 TYR cc_start: 0.8762 (t80) cc_final: 0.8555 (t80) REVERT: J 134 PHE cc_start: 0.8637 (m-80) cc_final: 0.8280 (m-10) REVERT: J 140 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8450 (ttp-110) REVERT: J 158 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8760 (mt-10) REVERT: K 20 ARG cc_start: 0.9149 (mmm160) cc_final: 0.8794 (mmt180) REVERT: K 21 ILE cc_start: 0.9217 (mt) cc_final: 0.8879 (mt) REVERT: K 39 ASN cc_start: 0.9095 (t0) cc_final: 0.8824 (t0) REVERT: K 44 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8323 (ptp-170) REVERT: K 73 GLN cc_start: 0.8809 (pp30) cc_final: 0.8341 (pp30) REVERT: K 74 ILE cc_start: 0.9634 (mm) cc_final: 0.9230 (mm) REVERT: K 89 MET cc_start: 0.9616 (mtt) cc_final: 0.9131 (mtm) REVERT: K 110 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8511 (mt-10) REVERT: K 134 PHE cc_start: 0.8740 (m-80) cc_final: 0.8434 (m-80) REVERT: K 140 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8421 (ttp-110) REVERT: K 144 LYS cc_start: 0.9225 (tppt) cc_final: 0.8742 (tppt) REVERT: L 48 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.7794 (ttm-80) REVERT: L 113 HIS cc_start: 0.9026 (m-70) cc_final: 0.8809 (m-70) REVERT: L 134 PHE cc_start: 0.8766 (m-80) cc_final: 0.8409 (m-10) REVERT: L 144 LYS cc_start: 0.8994 (tppt) cc_final: 0.8759 (tppt) REVERT: L 152 LYS cc_start: 0.9706 (ttpp) cc_final: 0.9407 (pttp) REVERT: L 162 PHE cc_start: 0.9550 (m-80) cc_final: 0.9239 (m-80) REVERT: M 20 ARG cc_start: 0.9218 (mmm160) cc_final: 0.8876 (mmt180) REVERT: M 21 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8660 (mt) REVERT: M 36 ILE cc_start: 0.9747 (mm) cc_final: 0.9423 (mm) REVERT: M 39 ASN cc_start: 0.8991 (t0) cc_final: 0.8423 (t0) REVERT: M 43 MET cc_start: 0.9264 (mmm) cc_final: 0.9002 (mmm) REVERT: M 51 GLU cc_start: 0.9299 (tm-30) cc_final: 0.8842 (tm-30) REVERT: M 52 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8856 (mm-40) REVERT: M 110 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8565 (mt-10) REVERT: N 39 ASN cc_start: 0.8930 (t0) cc_final: 0.8241 (t0) REVERT: N 43 MET cc_start: 0.9360 (mmm) cc_final: 0.9017 (mmm) REVERT: N 48 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8401 (ttm110) REVERT: N 89 MET cc_start: 0.9629 (mtt) cc_final: 0.9277 (mtp) REVERT: N 120 MET cc_start: 0.6688 (ppp) cc_final: 0.6486 (ppp) REVERT: N 134 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7804 (t80) REVERT: N 144 LYS cc_start: 0.8951 (tppt) cc_final: 0.8719 (tppt) REVERT: P 39 ASN cc_start: 0.8944 (t0) cc_final: 0.8235 (t0) REVERT: P 43 MET cc_start: 0.8817 (mmm) cc_final: 0.8384 (mmm) REVERT: P 48 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8396 (tpp80) REVERT: P 89 MET cc_start: 0.9398 (mtm) cc_final: 0.8473 (ttm) REVERT: P 99 TYR cc_start: 0.9343 (t80) cc_final: 0.9024 (t80) REVERT: P 113 HIS cc_start: 0.9053 (m-70) cc_final: 0.8826 (m-70) REVERT: P 152 LYS cc_start: 0.9729 (ttpp) cc_final: 0.9299 (pttp) REVERT: P 162 PHE cc_start: 0.9505 (m-80) cc_final: 0.9266 (m-80) REVERT: R 140 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8258 (ttp-110) REVERT: T 23 MET cc_start: 0.9010 (tpp) cc_final: 0.8772 (tpp) REVERT: T 89 MET cc_start: 0.9337 (mtm) cc_final: 0.8230 (mtp) REVERT: T 162 PHE cc_start: 0.9268 (m-80) cc_final: 0.9064 (m-80) REVERT: a 82 LEU cc_start: 0.9797 (OUTLIER) cc_final: 0.9576 (tp) REVERT: a 121 GLU cc_start: 0.9283 (mp0) cc_final: 0.8941 (pm20) REVERT: a 158 MET cc_start: 0.8232 (tpp) cc_final: 0.7928 (tpp) REVERT: b 39 GLN cc_start: 0.9252 (mm110) cc_final: 0.8819 (mm-40) REVERT: b 113 MET cc_start: 0.8834 (tmm) cc_final: 0.8362 (tmm) REVERT: b 158 MET cc_start: 0.9274 (tpp) cc_final: 0.8954 (tpp) REVERT: b 170 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7501 (mmm) REVERT: b 173 LYS cc_start: 0.8866 (pttt) cc_final: 0.8637 (ptpt) REVERT: d 126 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9325 (tp) REVERT: e 24 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9464 (mm) REVERT: e 27 ILE cc_start: 0.9612 (mm) cc_final: 0.9368 (tp) REVERT: e 38 GLN cc_start: 0.9189 (tp40) cc_final: 0.8940 (tp-100) REVERT: e 59 MET cc_start: 0.9218 (mmm) cc_final: 0.8898 (mmm) REVERT: e 63 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9234 (mp) REVERT: e 113 MET cc_start: 0.8974 (tmm) cc_final: 0.8529 (tmm) REVERT: e 121 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8596 (tm-30) REVERT: e 125 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8561 (mm-40) REVERT: e 158 MET cc_start: 0.9455 (tpp) cc_final: 0.9053 (tpp) REVERT: g 11 ASP cc_start: 0.8500 (m-30) cc_final: 0.8136 (m-30) REVERT: g 39 GLN cc_start: 0.9235 (mm110) cc_final: 0.8768 (mm-40) REVERT: g 158 MET cc_start: 0.9220 (tpp) cc_final: 0.8893 (tpp) REVERT: g 169 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8151 (pp) REVERT: g 171 LYS cc_start: 0.9324 (mtmm) cc_final: 0.9092 (tptp) REVERT: h 11 ASP cc_start: 0.8202 (m-30) cc_final: 0.7904 (m-30) REVERT: h 158 MET cc_start: 0.9040 (tpp) cc_final: 0.8680 (tpp) REVERT: i 125 GLN cc_start: 0.9176 (mp10) cc_final: 0.8903 (mp10) REVERT: i 158 MET cc_start: 0.9264 (tpp) cc_final: 0.8906 (tpp) REVERT: j 32 MET cc_start: 0.9127 (mmp) cc_final: 0.8859 (mmp) REVERT: j 82 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9402 (tp) REVERT: j 113 MET cc_start: 0.9170 (tpp) cc_final: 0.8802 (tpp) REVERT: j 126 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9197 (tp) REVERT: j 152 ASP cc_start: 0.9451 (m-30) cc_final: 0.9157 (m-30) REVERT: j 158 MET cc_start: 0.9324 (tpp) cc_final: 0.9048 (tpp) REVERT: k 58 LYS cc_start: 0.9331 (ttmm) cc_final: 0.9090 (tptp) REVERT: k 127 LYS cc_start: 0.9463 (ptpp) cc_final: 0.9069 (ptpt) REVERT: k 158 MET cc_start: 0.8845 (tpp) cc_final: 0.8573 (tpp) REVERT: k 195 LYS cc_start: 0.9337 (mppt) cc_final: 0.9065 (mppt) REVERT: k 199 ASP cc_start: 0.9231 (p0) cc_final: 0.8887 (p0) REVERT: l 125 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8929 (mm-40) REVERT: m 44 MET cc_start: 0.8718 (mmm) cc_final: 0.8496 (tpt) REVERT: m 96 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8598 (mt-10) REVERT: m 116 LYS cc_start: 0.9559 (mtmt) cc_final: 0.9307 (mtmm) REVERT: m 127 LYS cc_start: 0.9554 (pttp) cc_final: 0.9283 (pttp) REVERT: m 158 MET cc_start: 0.9112 (tpp) cc_final: 0.8741 (tpp) REVERT: m 170 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9060 (mtm) REVERT: m 171 LYS cc_start: 0.8970 (pttp) cc_final: 0.8662 (tptp) REVERT: n 44 MET cc_start: 0.8691 (mmm) cc_final: 0.8369 (mmm) REVERT: n 113 MET cc_start: 0.8925 (tpp) cc_final: 0.8704 (tpp) REVERT: n 170 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: p 11 ASP cc_start: 0.8745 (m-30) cc_final: 0.8190 (m-30) REVERT: p 38 GLN cc_start: 0.9188 (tp40) cc_final: 0.8970 (tp40) REVERT: p 187 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6078 (t80) REVERT: r 44 MET cc_start: 0.8884 (tpp) cc_final: 0.8574 (tpp) REVERT: r 127 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.9417 (ptpp) REVERT: r 158 MET cc_start: 0.8799 (tpp) cc_final: 0.8561 (tpp) REVERT: r 199 ASP cc_start: 0.9230 (p0) cc_final: 0.8937 (p0) REVERT: t 21 LYS cc_start: 0.9512 (mttt) cc_final: 0.8870 (tmtt) REVERT: t 39 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8729 (mm-40) REVERT: t 127 LYS cc_start: 0.9441 (pttm) cc_final: 0.9167 (ptpp) REVERT: t 152 ASP cc_start: 0.9391 (m-30) cc_final: 0.9171 (m-30) outliers start: 182 outliers final: 126 residues processed: 1361 average time/residue: 0.6018 time to fit residues: 1315.1135 Evaluate side-chains 1285 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1142 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 134 PHE Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 14 ASN Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 153 ASN Chi-restraints excluded: chain a residue 170 MET Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 188 SER Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 MET Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 35 LYS Chi-restraints excluded: chain d residue 38 GLN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 165 TYR Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 169 LEU Chi-restraints excluded: chain g residue 180 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 163 ASN Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 176 THR Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 144 HIS Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 180 HIS Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 153 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 170 MET Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 200 ILE Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 170 MET Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 28 PHE Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 97 THR Chi-restraints excluded: chain r residue 127 LYS Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain r residue 169 LEU Chi-restraints excluded: chain t residue 130 VAL Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 148 VAL Chi-restraints excluded: chain t residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 381 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 367 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 391 optimal weight: 0.9980 chunk 419 optimal weight: 40.0000 chunk 304 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 484 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 ASN b 43 ASN b 180 HIS ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 GLN g 38 GLN g 43 ASN h 43 ASN h 180 HIS ** j 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 43 ASN ** k 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 39 GLN t 43 ASN t 136 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 58327 Z= 0.251 Angle : 0.868 14.795 81125 Z= 0.471 Chirality : 0.044 0.224 9340 Planarity : 0.005 0.057 8642 Dihedral : 17.200 89.356 11967 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.18 % Allowed : 26.85 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 5950 helix: 0.51 (0.08), residues: 4335 sheet: 0.27 (0.33), residues: 204 loop : -2.51 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 117 HIS 0.016 0.001 HIS h 180 PHE 0.031 0.002 PHE K 162 TYR 0.035 0.002 TYR c 45 ARG 0.014 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1263 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 52 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8828 (mm-40) REVERT: A 89 MET cc_start: 0.9376 (mtm) cc_final: 0.8650 (mtp) REVERT: A 120 MET cc_start: 0.7650 (ppp) cc_final: 0.7274 (ppp) REVERT: A 140 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8274 (ttp-110) REVERT: A 150 MET cc_start: 0.8866 (mpp) cc_final: 0.8270 (pmm) REVERT: A 158 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8744 (mt-10) REVERT: A 162 PHE cc_start: 0.9584 (m-80) cc_final: 0.9210 (m-80) REVERT: B 39 ASN cc_start: 0.9173 (t0) cc_final: 0.8765 (t0) REVERT: B 51 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 52 GLN cc_start: 0.9262 (mm-40) cc_final: 0.7934 (mm-40) REVERT: B 84 TYR cc_start: 0.8788 (m-80) cc_final: 0.8430 (m-80) REVERT: B 99 TYR cc_start: 0.8887 (t80) cc_final: 0.7422 (t80) REVERT: B 108 LEU cc_start: 0.9519 (pt) cc_final: 0.9259 (mt) REVERT: B 120 MET cc_start: 0.7604 (ppp) cc_final: 0.7363 (ppp) REVERT: C 28 THR cc_start: 0.9348 (m) cc_final: 0.9129 (m) REVERT: C 39 ASN cc_start: 0.8782 (t0) cc_final: 0.8414 (t0) REVERT: C 51 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8629 (tm-30) REVERT: C 52 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8724 (mm-40) REVERT: C 89 MET cc_start: 0.9378 (mtm) cc_final: 0.9142 (mtm) REVERT: C 134 PHE cc_start: 0.8322 (m-80) cc_final: 0.7982 (m-10) REVERT: D 39 ASN cc_start: 0.8869 (t0) cc_final: 0.8445 (t0) REVERT: D 89 MET cc_start: 0.9245 (mtp) cc_final: 0.8983 (mtp) REVERT: D 94 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.8888 (tptt) REVERT: D 134 PHE cc_start: 0.8517 (m-80) cc_final: 0.8212 (m-10) REVERT: E 17 TYR cc_start: 0.8949 (t80) cc_final: 0.8562 (t80) REVERT: E 21 ILE cc_start: 0.9060 (mt) cc_final: 0.8737 (mt) REVERT: E 39 ASN cc_start: 0.8778 (t0) cc_final: 0.8200 (t0) REVERT: E 89 MET cc_start: 0.9459 (mtm) cc_final: 0.8939 (mtm) REVERT: E 162 PHE cc_start: 0.9570 (m-80) cc_final: 0.9341 (m-80) REVERT: F 27 THR cc_start: 0.8734 (m) cc_final: 0.8477 (m) REVERT: F 39 ASN cc_start: 0.9140 (t0) cc_final: 0.8612 (t0) REVERT: F 48 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8287 (ttm110) REVERT: F 51 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8827 (tm-30) REVERT: F 52 GLN cc_start: 0.9481 (mm-40) cc_final: 0.8907 (mm-40) REVERT: F 55 TYR cc_start: 0.9128 (t80) cc_final: 0.8873 (t80) REVERT: F 134 PHE cc_start: 0.8497 (m-80) cc_final: 0.8208 (m-10) REVERT: F 144 LYS cc_start: 0.9064 (tppt) cc_final: 0.8838 (tppt) REVERT: F 162 PHE cc_start: 0.9416 (m-80) cc_final: 0.9140 (m-80) REVERT: G 27 THR cc_start: 0.9048 (m) cc_final: 0.8607 (p) REVERT: G 84 TYR cc_start: 0.8788 (m-80) cc_final: 0.8274 (m-80) REVERT: G 89 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9066 (ttp) REVERT: G 96 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9566 (pp) REVERT: G 111 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9339 (tp) REVERT: G 162 PHE cc_start: 0.9582 (m-80) cc_final: 0.9015 (m-80) REVERT: H 43 MET cc_start: 0.9370 (mmm) cc_final: 0.9161 (mmm) REVERT: H 48 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8553 (ttm110) REVERT: H 73 GLN cc_start: 0.9090 (pp30) cc_final: 0.8885 (pp30) REVERT: H 89 MET cc_start: 0.9375 (mtt) cc_final: 0.9034 (mtm) REVERT: H 113 HIS cc_start: 0.9209 (m90) cc_final: 0.8748 (m90) REVERT: H 120 MET cc_start: 0.7619 (ppp) cc_final: 0.7189 (ppp) REVERT: H 134 PHE cc_start: 0.8454 (m-80) cc_final: 0.8036 (m-10) REVERT: H 140 ARG cc_start: 0.8806 (ttp-110) cc_final: 0.8499 (ttp-110) REVERT: H 152 LYS cc_start: 0.9742 (ttpp) cc_final: 0.9418 (pttp) REVERT: H 162 PHE cc_start: 0.9564 (m-80) cc_final: 0.9319 (m-80) REVERT: I 39 ASN cc_start: 0.9167 (t0) cc_final: 0.8724 (t0) REVERT: I 51 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8868 (tm-30) REVERT: I 84 TYR cc_start: 0.8890 (m-80) cc_final: 0.8103 (m-80) REVERT: I 89 MET cc_start: 0.9624 (mtt) cc_final: 0.9298 (mtp) REVERT: I 110 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8398 (tt0) REVERT: I 144 LYS cc_start: 0.8923 (tppt) cc_final: 0.8606 (tppt) REVERT: I 150 MET cc_start: 0.9353 (mmm) cc_final: 0.8758 (mpp) REVERT: I 158 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8999 (mt-10) REVERT: I 162 PHE cc_start: 0.9590 (m-80) cc_final: 0.9202 (m-80) REVERT: J 39 ASN cc_start: 0.8614 (t0) cc_final: 0.8136 (t0) REVERT: J 43 MET cc_start: 0.9167 (mmm) cc_final: 0.8766 (mmm) REVERT: J 48 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8268 (tpp80) REVERT: J 53 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7769 (mt-10) REVERT: J 73 GLN cc_start: 0.8956 (pp30) cc_final: 0.8671 (pp30) REVERT: J 74 ILE cc_start: 0.9755 (mm) cc_final: 0.9501 (mm) REVERT: J 99 TYR cc_start: 0.8894 (t80) cc_final: 0.8615 (t80) REVERT: J 117 TRP cc_start: 0.8650 (t-100) cc_final: 0.8416 (t-100) REVERT: J 120 MET cc_start: 0.8393 (ppp) cc_final: 0.7942 (ppp) REVERT: J 134 PHE cc_start: 0.8586 (m-80) cc_final: 0.8260 (m-10) REVERT: J 140 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8396 (ttp-110) REVERT: J 144 LYS cc_start: 0.9270 (tppt) cc_final: 0.8925 (tppt) REVERT: J 158 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8817 (mt-10) REVERT: K 20 ARG cc_start: 0.9147 (mmm160) cc_final: 0.8717 (mmt180) REVERT: K 21 ILE cc_start: 0.9143 (mt) cc_final: 0.8803 (mt) REVERT: K 39 ASN cc_start: 0.9032 (t0) cc_final: 0.8713 (t0) REVERT: K 44 ARG cc_start: 0.8630 (mtm-85) cc_final: 0.8254 (ptp-170) REVERT: K 89 MET cc_start: 0.9606 (mtt) cc_final: 0.9285 (mtm) REVERT: K 110 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8563 (mt-10) REVERT: K 134 PHE cc_start: 0.8665 (m-80) cc_final: 0.8369 (m-10) REVERT: K 140 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8430 (ttp-110) REVERT: K 144 LYS cc_start: 0.9218 (tppt) cc_final: 0.8734 (tppt) REVERT: L 43 MET cc_start: 0.8994 (mmm) cc_final: 0.8741 (mmm) REVERT: L 44 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8362 (mtt180) REVERT: L 78 TYR cc_start: 0.8849 (m-10) cc_final: 0.8622 (m-10) REVERT: L 113 HIS cc_start: 0.9056 (m-70) cc_final: 0.8836 (m-70) REVERT: L 134 PHE cc_start: 0.8775 (m-80) cc_final: 0.8464 (m-10) REVERT: L 144 LYS cc_start: 0.9004 (tppt) cc_final: 0.8760 (tppt) REVERT: L 152 LYS cc_start: 0.9660 (ttpp) cc_final: 0.9373 (pttp) REVERT: L 162 PHE cc_start: 0.9516 (m-80) cc_final: 0.9199 (m-80) REVERT: M 20 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8854 (mmt180) REVERT: M 21 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8596 (mt) REVERT: M 36 ILE cc_start: 0.9746 (mm) cc_final: 0.9406 (mm) REVERT: M 39 ASN cc_start: 0.8944 (t0) cc_final: 0.8274 (t0) REVERT: M 43 MET cc_start: 0.9279 (mmm) cc_final: 0.9034 (mmm) REVERT: M 51 GLU cc_start: 0.9286 (tm-30) cc_final: 0.8823 (tm-30) REVERT: M 52 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8836 (mm-40) REVERT: M 110 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8547 (mt-10) REVERT: M 162 PHE cc_start: 0.9367 (m-80) cc_final: 0.8808 (m-80) REVERT: N 39 ASN cc_start: 0.8817 (t0) cc_final: 0.8301 (t0) REVERT: N 43 MET cc_start: 0.9319 (mmm) cc_final: 0.9009 (mmm) REVERT: N 48 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8387 (ttm110) REVERT: N 89 MET cc_start: 0.9594 (mtt) cc_final: 0.9301 (mtp) REVERT: N 144 LYS cc_start: 0.9022 (tppt) cc_final: 0.8806 (tppt) REVERT: P 39 ASN cc_start: 0.9010 (t0) cc_final: 0.8431 (t0) REVERT: P 41 GLU cc_start: 0.8706 (pm20) cc_final: 0.7927 (pm20) REVERT: P 48 ARG cc_start: 0.8953 (tpp80) cc_final: 0.8472 (tpp80) REVERT: P 99 TYR cc_start: 0.9334 (t80) cc_final: 0.9031 (t80) REVERT: P 152 LYS cc_start: 0.9740 (ttpp) cc_final: 0.9305 (pttp) REVERT: P 162 PHE cc_start: 0.9490 (m-80) cc_final: 0.9267 (m-80) REVERT: R 48 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8799 (tpp80) REVERT: R 89 MET cc_start: 0.9337 (mtp) cc_final: 0.8793 (ptm) REVERT: R 140 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8334 (ttp-110) REVERT: R 144 LYS cc_start: 0.9113 (tppt) cc_final: 0.8872 (tppt) REVERT: R 162 PHE cc_start: 0.9258 (m-80) cc_final: 0.8851 (m-80) REVERT: T 51 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8707 (tm-30) REVERT: T 89 MET cc_start: 0.9300 (mtm) cc_final: 0.8994 (mtm) REVERT: T 110 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8739 (tt0) REVERT: a 25 TYR cc_start: 0.9269 (t80) cc_final: 0.9015 (t80) REVERT: a 82 LEU cc_start: 0.9782 (OUTLIER) cc_final: 0.9566 (tp) REVERT: b 113 MET cc_start: 0.8832 (tmm) cc_final: 0.8361 (tmm) REVERT: b 158 MET cc_start: 0.9247 (tpp) cc_final: 0.8904 (tpp) REVERT: b 170 MET cc_start: 0.8573 (mtm) cc_final: 0.7495 (mmm) REVERT: b 173 LYS cc_start: 0.8839 (pttt) cc_final: 0.8602 (ptpt) REVERT: c 152 ASP cc_start: 0.9434 (m-30) cc_final: 0.9190 (m-30) REVERT: d 126 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9146 (tp) REVERT: e 24 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9421 (mm) REVERT: e 27 ILE cc_start: 0.9574 (mm) cc_final: 0.9235 (tp) REVERT: e 38 GLN cc_start: 0.9200 (tp40) cc_final: 0.8932 (tp-100) REVERT: e 39 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8616 (mm-40) REVERT: e 59 MET cc_start: 0.9214 (mmm) cc_final: 0.8846 (mmm) REVERT: e 63 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9162 (mp) REVERT: e 113 MET cc_start: 0.8995 (tmm) cc_final: 0.8540 (tmm) REVERT: e 121 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8865 (tm-30) REVERT: e 158 MET cc_start: 0.9422 (tpp) cc_final: 0.9000 (tpp) REVERT: f 44 MET cc_start: 0.8997 (ttm) cc_final: 0.8675 (ttm) REVERT: f 152 ASP cc_start: 0.9360 (m-30) cc_final: 0.9108 (m-30) REVERT: f 158 MET cc_start: 0.8901 (tpp) cc_final: 0.8685 (tpp) REVERT: g 11 ASP cc_start: 0.8389 (m-30) cc_final: 0.7965 (m-30) REVERT: g 127 LYS cc_start: 0.9411 (pttm) cc_final: 0.9103 (ptpp) REVERT: g 152 ASP cc_start: 0.9365 (m-30) cc_final: 0.9065 (m-30) REVERT: g 158 MET cc_start: 0.9202 (tpp) cc_final: 0.8968 (tpp) REVERT: h 11 ASP cc_start: 0.8086 (m-30) cc_final: 0.7761 (m-30) REVERT: h 158 MET cc_start: 0.8986 (tpp) cc_final: 0.8606 (tpp) REVERT: i 127 LYS cc_start: 0.9589 (pttp) cc_final: 0.9379 (ptpp) REVERT: i 158 MET cc_start: 0.9230 (tpp) cc_final: 0.8871 (tpp) REVERT: i 201 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7632 (mm-30) REVERT: j 82 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9432 (tp) REVERT: j 113 MET cc_start: 0.9134 (tpp) cc_final: 0.8784 (tpp) REVERT: j 126 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9056 (tp) REVERT: j 158 MET cc_start: 0.9281 (tpp) cc_final: 0.9057 (tpp) REVERT: k 58 LYS cc_start: 0.9378 (ttmm) cc_final: 0.9064 (tptp) REVERT: k 158 MET cc_start: 0.8929 (tpp) cc_final: 0.8702 (tpp) REVERT: k 195 LYS cc_start: 0.9276 (mppt) cc_final: 0.9054 (mppt) REVERT: k 201 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8113 (mm-30) REVERT: l 96 GLU cc_start: 0.8917 (mp0) cc_final: 0.8563 (mp0) REVERT: l 125 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9118 (mm-40) REVERT: m 96 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8631 (mt-10) REVERT: m 127 LYS cc_start: 0.9551 (pttp) cc_final: 0.9301 (pttp) REVERT: m 158 MET cc_start: 0.9221 (tpp) cc_final: 0.8775 (tpp) REVERT: m 170 MET cc_start: 0.9216 (mtm) cc_final: 0.8993 (mtm) REVERT: m 171 LYS cc_start: 0.9095 (pttp) cc_final: 0.8665 (tppt) REVERT: m 198 GLU cc_start: 0.9236 (pt0) cc_final: 0.8967 (tp30) REVERT: n 44 MET cc_start: 0.8721 (mmm) cc_final: 0.8376 (mmm) REVERT: n 113 MET cc_start: 0.8887 (tpp) cc_final: 0.8642 (tpp) REVERT: n 127 LYS cc_start: 0.9592 (pttp) cc_final: 0.9339 (ptpp) REVERT: n 135 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7382 (mp0) REVERT: n 170 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8138 (mtm) REVERT: p 11 ASP cc_start: 0.8737 (m-30) cc_final: 0.8188 (m-30) REVERT: p 38 GLN cc_start: 0.9180 (tp40) cc_final: 0.8710 (tp40) REVERT: p 127 LYS cc_start: 0.9497 (pttp) cc_final: 0.9010 (ptpt) REVERT: p 187 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6095 (t80) REVERT: r 34 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7549 (tm-30) REVERT: r 38 GLN cc_start: 0.9275 (tp40) cc_final: 0.8994 (tp40) REVERT: r 121 GLU cc_start: 0.9485 (mp0) cc_final: 0.9231 (pm20) REVERT: r 199 ASP cc_start: 0.9173 (p0) cc_final: 0.8881 (p0) REVERT: t 21 LYS cc_start: 0.9508 (mttt) cc_final: 0.8860 (tmtt) REVERT: t 127 LYS cc_start: 0.9424 (pttm) cc_final: 0.9156 (ptpp) REVERT: t 152 ASP cc_start: 0.9283 (m-30) cc_final: 0.9019 (m-30) outliers start: 159 outliers final: 121 residues processed: 1355 average time/residue: 0.6011 time to fit residues: 1310.4923 Evaluate side-chains 1278 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1144 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 188 SER Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 165 TYR Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 180 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 163 ASN Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 148 VAL Chi-restraints excluded: chain i residue 176 THR Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain j residue 168 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 129 LEU Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 180 HIS Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 137 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 153 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 200 ILE Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 170 MET Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain p residue 129 LEU Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 97 THR Chi-restraints excluded: chain r residue 127 LYS Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain t residue 130 VAL Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 148 VAL Chi-restraints excluded: chain t residue 168 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 560 optimal weight: 9.9990 chunk 590 optimal weight: 20.0000 chunk 538 optimal weight: 8.9990 chunk 573 optimal weight: 0.9990 chunk 589 optimal weight: 8.9990 chunk 345 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 450 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 518 optimal weight: 10.0000 chunk 542 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN T 65 HIS ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 HIS ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN h 43 ASN h 125 GLN h 180 HIS ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 ASN k 144 HIS n 38 GLN n 136 GLN r 124 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 58327 Z= 0.257 Angle : 0.906 15.178 81125 Z= 0.489 Chirality : 0.045 0.229 9340 Planarity : 0.005 0.057 8642 Dihedral : 17.198 83.959 11967 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.22 % Allowed : 27.95 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5950 helix: 0.36 (0.08), residues: 4403 sheet: 0.29 (0.34), residues: 204 loop : -2.46 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 117 HIS 0.020 0.001 HIS h 180 PHE 0.024 0.002 PHE T 162 TYR 0.034 0.002 TYR c 45 ARG 0.014 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1231 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8552 (tm-30) REVERT: A 52 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8825 (mm-40) REVERT: A 89 MET cc_start: 0.9377 (mtm) cc_final: 0.8722 (mtp) REVERT: A 120 MET cc_start: 0.7983 (ppp) cc_final: 0.7566 (ppp) REVERT: A 140 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8277 (ttp-110) REVERT: A 150 MET cc_start: 0.8811 (mpp) cc_final: 0.8197 (pmm) REVERT: A 162 PHE cc_start: 0.9587 (m-80) cc_final: 0.9228 (m-80) REVERT: B 39 ASN cc_start: 0.9147 (t0) cc_final: 0.8823 (t0) REVERT: B 52 GLN cc_start: 0.9239 (mm-40) cc_final: 0.9000 (tm-30) REVERT: B 84 TYR cc_start: 0.8789 (m-80) cc_final: 0.8382 (m-80) REVERT: B 99 TYR cc_start: 0.8933 (t80) cc_final: 0.7414 (t80) REVERT: B 108 LEU cc_start: 0.9520 (pt) cc_final: 0.9277 (mt) REVERT: B 120 MET cc_start: 0.7729 (ppp) cc_final: 0.7496 (ppp) REVERT: C 39 ASN cc_start: 0.8786 (t0) cc_final: 0.8478 (t0) REVERT: C 51 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 52 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8718 (mm-40) REVERT: C 89 MET cc_start: 0.9369 (mtm) cc_final: 0.9125 (mtm) REVERT: C 134 PHE cc_start: 0.8459 (m-80) cc_final: 0.8147 (m-10) REVERT: D 39 ASN cc_start: 0.8925 (t0) cc_final: 0.8147 (t0) REVERT: D 89 MET cc_start: 0.9240 (mtp) cc_final: 0.8983 (mtp) REVERT: D 94 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.8869 (tppt) REVERT: D 134 PHE cc_start: 0.8635 (m-80) cc_final: 0.8332 (m-10) REVERT: E 17 TYR cc_start: 0.8965 (t80) cc_final: 0.8598 (t80) REVERT: E 21 ILE cc_start: 0.9068 (mt) cc_final: 0.8759 (mt) REVERT: E 39 ASN cc_start: 0.8595 (t0) cc_final: 0.8311 (t0) REVERT: E 89 MET cc_start: 0.9442 (mtm) cc_final: 0.8944 (mtm) REVERT: E 135 ILE cc_start: 0.8377 (mm) cc_final: 0.8119 (tp) REVERT: E 162 PHE cc_start: 0.9557 (m-80) cc_final: 0.9318 (m-80) REVERT: F 27 THR cc_start: 0.8700 (m) cc_final: 0.8467 (m) REVERT: F 39 ASN cc_start: 0.9105 (t0) cc_final: 0.8707 (t0) REVERT: F 48 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8340 (ttm110) REVERT: F 51 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8809 (tm-30) REVERT: F 52 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8917 (mm-40) REVERT: F 55 TYR cc_start: 0.9101 (t80) cc_final: 0.8842 (t80) REVERT: F 134 PHE cc_start: 0.8536 (m-80) cc_final: 0.8265 (m-10) REVERT: F 162 PHE cc_start: 0.9407 (m-80) cc_final: 0.9092 (m-80) REVERT: G 27 THR cc_start: 0.9042 (m) cc_final: 0.8630 (p) REVERT: G 77 LYS cc_start: 0.8670 (tmmt) cc_final: 0.8370 (tmmt) REVERT: G 84 TYR cc_start: 0.8809 (m-80) cc_final: 0.8224 (m-80) REVERT: G 89 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9051 (ttp) REVERT: G 96 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9502 (pp) REVERT: G 111 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9335 (tp) REVERT: G 144 LYS cc_start: 0.9135 (tppt) cc_final: 0.8848 (tppt) REVERT: G 162 PHE cc_start: 0.9600 (m-80) cc_final: 0.8986 (m-80) REVERT: H 43 MET cc_start: 0.9364 (mmm) cc_final: 0.9145 (mmm) REVERT: H 48 ARG cc_start: 0.8949 (ttm110) cc_final: 0.8502 (ttm110) REVERT: H 89 MET cc_start: 0.9374 (mtt) cc_final: 0.9031 (mtm) REVERT: H 113 HIS cc_start: 0.9211 (m90) cc_final: 0.8754 (m90) REVERT: H 120 MET cc_start: 0.7622 (ppp) cc_final: 0.7194 (ppp) REVERT: H 134 PHE cc_start: 0.8438 (m-80) cc_final: 0.8015 (m-10) REVERT: H 140 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8511 (ttp-110) REVERT: I 39 ASN cc_start: 0.9133 (t0) cc_final: 0.8700 (t0) REVERT: I 51 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8872 (tm-30) REVERT: I 84 TYR cc_start: 0.8870 (m-80) cc_final: 0.8083 (m-80) REVERT: I 89 MET cc_start: 0.9606 (mtt) cc_final: 0.9303 (mtp) REVERT: I 110 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8666 (tt0) REVERT: I 120 MET cc_start: 0.7283 (ppp) cc_final: 0.7003 (ppp) REVERT: I 144 LYS cc_start: 0.8941 (tppt) cc_final: 0.8619 (tppt) REVERT: I 150 MET cc_start: 0.9292 (mmm) cc_final: 0.8970 (mpp) REVERT: I 162 PHE cc_start: 0.9572 (m-80) cc_final: 0.9210 (m-80) REVERT: J 39 ASN cc_start: 0.8737 (t0) cc_final: 0.8274 (t0) REVERT: J 43 MET cc_start: 0.9109 (mmm) cc_final: 0.8741 (mmm) REVERT: J 48 ARG cc_start: 0.8690 (ttm110) cc_final: 0.8169 (tpp80) REVERT: J 53 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7670 (mm-30) REVERT: J 64 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8856 (p) REVERT: J 73 GLN cc_start: 0.9019 (pp30) cc_final: 0.8720 (pp30) REVERT: J 74 ILE cc_start: 0.9747 (mm) cc_final: 0.9512 (mm) REVERT: J 110 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8694 (tt0) REVERT: J 113 HIS cc_start: 0.8715 (m-70) cc_final: 0.8497 (m-70) REVERT: J 117 TRP cc_start: 0.8694 (t-100) cc_final: 0.8373 (t-100) REVERT: J 120 MET cc_start: 0.8413 (ppp) cc_final: 0.8002 (ppp) REVERT: J 134 PHE cc_start: 0.8600 (m-80) cc_final: 0.8244 (m-10) REVERT: J 140 ARG cc_start: 0.8846 (ttp-110) cc_final: 0.8354 (ttp-110) REVERT: J 144 LYS cc_start: 0.9260 (tppt) cc_final: 0.9016 (tppt) REVERT: K 21 ILE cc_start: 0.9152 (mt) cc_final: 0.8817 (mt) REVERT: K 39 ASN cc_start: 0.9047 (t0) cc_final: 0.8750 (t0) REVERT: K 73 GLN cc_start: 0.8933 (pp30) cc_final: 0.8529 (pp30) REVERT: K 74 ILE cc_start: 0.9624 (mm) cc_final: 0.9336 (mm) REVERT: K 89 MET cc_start: 0.9598 (mtt) cc_final: 0.9291 (mtm) REVERT: K 110 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8545 (mt-10) REVERT: K 134 PHE cc_start: 0.8700 (m-80) cc_final: 0.8363 (m-10) REVERT: K 140 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8428 (ttp-110) REVERT: K 144 LYS cc_start: 0.9212 (tppt) cc_final: 0.8710 (tppt) REVERT: L 43 MET cc_start: 0.9067 (mmm) cc_final: 0.8812 (mmm) REVERT: L 113 HIS cc_start: 0.8992 (m-70) cc_final: 0.8757 (m-70) REVERT: L 134 PHE cc_start: 0.8784 (m-80) cc_final: 0.8482 (m-10) REVERT: L 144 LYS cc_start: 0.9021 (tppt) cc_final: 0.8761 (tppt) REVERT: L 152 LYS cc_start: 0.9683 (ttpp) cc_final: 0.9377 (pttp) REVERT: L 162 PHE cc_start: 0.9515 (m-80) cc_final: 0.9110 (m-80) REVERT: M 20 ARG cc_start: 0.9169 (mmm160) cc_final: 0.8862 (mmt180) REVERT: M 21 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8588 (mt) REVERT: M 36 ILE cc_start: 0.9736 (mm) cc_final: 0.9460 (mm) REVERT: M 39 ASN cc_start: 0.9131 (t0) cc_final: 0.8731 (t0) REVERT: M 43 MET cc_start: 0.9245 (mmm) cc_final: 0.9011 (mmm) REVERT: M 44 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8308 (ptp90) REVERT: M 51 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8824 (tm-30) REVERT: M 52 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8832 (mm-40) REVERT: M 162 PHE cc_start: 0.9371 (m-80) cc_final: 0.9160 (m-80) REVERT: N 39 ASN cc_start: 0.8769 (t0) cc_final: 0.8345 (t0) REVERT: N 43 MET cc_start: 0.9337 (mmm) cc_final: 0.8993 (mmm) REVERT: N 48 ARG cc_start: 0.8974 (ttm-80) cc_final: 0.8438 (ttm110) REVERT: N 69 GLU cc_start: 0.9269 (pp20) cc_final: 0.9037 (pp20) REVERT: N 89 MET cc_start: 0.9568 (mtt) cc_final: 0.9279 (mtp) REVERT: N 140 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8424 (ttp-110) REVERT: P 39 ASN cc_start: 0.8904 (t0) cc_final: 0.8556 (t0) REVERT: P 48 ARG cc_start: 0.9030 (tpp80) cc_final: 0.8482 (tpp80) REVERT: P 99 TYR cc_start: 0.9332 (t80) cc_final: 0.9038 (t80) REVERT: P 150 MET cc_start: 0.8799 (mpp) cc_final: 0.8303 (pmm) REVERT: P 162 PHE cc_start: 0.9505 (m-80) cc_final: 0.9298 (m-80) REVERT: R 48 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8811 (tpp80) REVERT: R 89 MET cc_start: 0.9337 (mtp) cc_final: 0.8791 (ptm) REVERT: R 99 TYR cc_start: 0.8892 (t80) cc_final: 0.8681 (t80) REVERT: R 113 HIS cc_start: 0.8939 (m-70) cc_final: 0.8738 (m-70) REVERT: R 150 MET cc_start: 0.9236 (mmm) cc_final: 0.9015 (mpp) REVERT: T 51 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8798 (tm-30) REVERT: T 89 MET cc_start: 0.9291 (mtm) cc_final: 0.8984 (mtm) REVERT: T 110 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8813 (tt0) REVERT: T 134 PHE cc_start: 0.8431 (m-80) cc_final: 0.8178 (m-80) REVERT: T 162 PHE cc_start: 0.9340 (m-80) cc_final: 0.8634 (m-80) REVERT: a 82 LEU cc_start: 0.9790 (OUTLIER) cc_final: 0.9582 (tp) REVERT: a 127 LYS cc_start: 0.9377 (ptpp) cc_final: 0.9162 (ptpp) REVERT: a 152 ASP cc_start: 0.9385 (m-30) cc_final: 0.9175 (m-30) REVERT: b 113 MET cc_start: 0.8818 (tmm) cc_final: 0.8366 (tmm) REVERT: b 125 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8856 (mp10) REVERT: b 158 MET cc_start: 0.9237 (tpp) cc_final: 0.8868 (tpp) REVERT: b 170 MET cc_start: 0.8624 (mtm) cc_final: 0.7685 (mmm) REVERT: c 38 GLN cc_start: 0.9259 (tp40) cc_final: 0.8981 (tp40) REVERT: d 59 MET cc_start: 0.9117 (mmm) cc_final: 0.6711 (mmm) REVERT: d 126 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8752 (tp) REVERT: d 171 LYS cc_start: 0.9028 (mttt) cc_final: 0.8816 (mttt) REVERT: e 24 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9443 (mm) REVERT: e 27 ILE cc_start: 0.9556 (mm) cc_final: 0.9228 (tp) REVERT: e 38 GLN cc_start: 0.9226 (tp40) cc_final: 0.8934 (tp-100) REVERT: e 39 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8640 (mm-40) REVERT: e 59 MET cc_start: 0.9208 (mmm) cc_final: 0.8827 (mmm) REVERT: e 113 MET cc_start: 0.8981 (tmm) cc_final: 0.8534 (tmm) REVERT: e 125 GLN cc_start: 0.9380 (mm-40) cc_final: 0.9160 (mp10) REVERT: e 127 LYS cc_start: 0.9533 (ptpp) cc_final: 0.9188 (pttm) REVERT: e 158 MET cc_start: 0.9438 (tpp) cc_final: 0.9034 (tpp) REVERT: f 44 MET cc_start: 0.8966 (ttm) cc_final: 0.8656 (ttm) REVERT: g 11 ASP cc_start: 0.8391 (m-30) cc_final: 0.7948 (m-30) REVERT: g 39 GLN cc_start: 0.9196 (mm110) cc_final: 0.8859 (mm-40) REVERT: g 127 LYS cc_start: 0.9468 (pttm) cc_final: 0.9134 (ptpp) REVERT: g 152 ASP cc_start: 0.9369 (m-30) cc_final: 0.9078 (m-30) REVERT: g 158 MET cc_start: 0.9210 (tpp) cc_final: 0.8961 (tpp) REVERT: g 174 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8933 (p) REVERT: h 11 ASP cc_start: 0.7969 (m-30) cc_final: 0.7700 (m-30) REVERT: h 127 LYS cc_start: 0.9629 (pttm) cc_final: 0.9316 (ptpp) REVERT: h 158 MET cc_start: 0.9060 (tpp) cc_final: 0.8707 (tpp) REVERT: i 158 MET cc_start: 0.9247 (tpp) cc_final: 0.8898 (tpp) REVERT: j 82 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9423 (tp) REVERT: j 113 MET cc_start: 0.9134 (tpp) cc_final: 0.8789 (tpp) REVERT: j 126 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8996 (tp) REVERT: j 170 MET cc_start: 0.8845 (mtm) cc_final: 0.8617 (mtm) REVERT: k 38 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8852 (tp-100) REVERT: k 58 LYS cc_start: 0.9393 (ttmm) cc_final: 0.9062 (tptp) REVERT: k 127 LYS cc_start: 0.9380 (ptpt) cc_final: 0.8985 (ptpt) REVERT: k 158 MET cc_start: 0.8899 (tpp) cc_final: 0.8689 (tpp) REVERT: l 27 ILE cc_start: 0.9335 (mm) cc_final: 0.9070 (mt) REVERT: l 96 GLU cc_start: 0.8912 (mp0) cc_final: 0.8395 (mp0) REVERT: l 199 ASP cc_start: 0.9038 (p0) cc_final: 0.8751 (p0) REVERT: m 59 MET cc_start: 0.9169 (mmm) cc_final: 0.8837 (mmp) REVERT: m 96 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8619 (mt-10) REVERT: m 127 LYS cc_start: 0.9559 (pttp) cc_final: 0.9267 (pttp) REVERT: m 158 MET cc_start: 0.9236 (tpp) cc_final: 0.8856 (tpp) REVERT: m 170 MET cc_start: 0.9181 (mtm) cc_final: 0.8927 (mtm) REVERT: m 171 LYS cc_start: 0.9140 (pttp) cc_final: 0.8732 (tppt) REVERT: m 198 GLU cc_start: 0.9190 (pt0) cc_final: 0.8905 (tp30) REVERT: n 44 MET cc_start: 0.8695 (mmm) cc_final: 0.8349 (mmm) REVERT: n 113 MET cc_start: 0.8845 (tpp) cc_final: 0.8481 (tpp) REVERT: n 116 LYS cc_start: 0.9635 (mtmt) cc_final: 0.9290 (mtmm) REVERT: n 127 LYS cc_start: 0.9578 (pttp) cc_final: 0.9248 (ptpp) REVERT: n 135 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7318 (mp0) REVERT: p 11 ASP cc_start: 0.8742 (m-30) cc_final: 0.8183 (m-30) REVERT: p 38 GLN cc_start: 0.9225 (tp40) cc_final: 0.8794 (tp40) REVERT: p 127 LYS cc_start: 0.9531 (pttp) cc_final: 0.9015 (ptpt) REVERT: p 187 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6099 (t80) REVERT: r 34 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7665 (tm-30) REVERT: r 38 GLN cc_start: 0.9330 (tp40) cc_final: 0.8933 (tp40) REVERT: r 42 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7485 (mm-30) REVERT: r 44 MET cc_start: 0.8745 (tpp) cc_final: 0.8401 (tpt) REVERT: r 121 GLU cc_start: 0.9484 (mp0) cc_final: 0.9221 (pm20) REVERT: r 199 ASP cc_start: 0.9149 (p0) cc_final: 0.8880 (p0) REVERT: t 21 LYS cc_start: 0.9509 (mttt) cc_final: 0.8867 (tmtt) REVERT: t 59 MET cc_start: 0.8895 (mmp) cc_final: 0.8607 (mmm) REVERT: t 127 LYS cc_start: 0.9422 (pttm) cc_final: 0.9188 (ptpp) REVERT: t 152 ASP cc_start: 0.9296 (m-30) cc_final: 0.9035 (m-30) REVERT: t 199 ASP cc_start: 0.9330 (p0) cc_final: 0.9066 (p0) outliers start: 161 outliers final: 127 residues processed: 1325 average time/residue: 0.6048 time to fit residues: 1292.0628 Evaluate side-chains 1276 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1136 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 82 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 188 SER Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 165 TYR Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 180 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 125 GLN Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 163 ASN Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain h residue 198 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 148 VAL Chi-restraints excluded: chain i residue 176 THR Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain j residue 168 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 126 LEU Chi-restraints excluded: chain k residue 129 LEU Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 144 HIS Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 180 HIS Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 153 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 200 ILE Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain n residue 136 GLN Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 170 MET Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain p residue 129 LEU Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain t residue 97 THR Chi-restraints excluded: chain t residue 130 VAL Chi-restraints excluded: chain t residue 135 GLU Chi-restraints excluded: chain t residue 148 VAL Chi-restraints excluded: chain t residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 571 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 606 optimal weight: 7.9990 chunk 370 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 421 optimal weight: 9.9990 chunk 636 optimal weight: 0.6980 chunk 585 optimal weight: 5.9990 chunk 506 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 391 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 HIS ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 136 GLN g 43 ASN h 39 GLN h 125 GLN h 180 HIS ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 144 HIS n 43 ASN ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 58327 Z= 0.265 Angle : 0.939 18.156 81125 Z= 0.506 Chirality : 0.046 0.211 9340 Planarity : 0.005 0.057 8642 Dihedral : 17.195 78.251 11967 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.88 % Allowed : 28.67 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 5950 helix: 0.25 (0.08), residues: 4420 sheet: 0.31 (0.34), residues: 204 loop : -2.38 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 117 HIS 0.021 0.001 HIS h 180 PHE 0.023 0.002 PHE T 162 TYR 0.033 0.002 TYR c 45 ARG 0.014 0.001 ARG L 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1214 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8549 (tm-30) REVERT: A 52 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8824 (mm-40) REVERT: A 89 MET cc_start: 0.9386 (mtm) cc_final: 0.8629 (mtp) REVERT: A 120 MET cc_start: 0.8107 (ppp) cc_final: 0.7738 (ppp) REVERT: A 140 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: A 150 MET cc_start: 0.8798 (mpp) cc_final: 0.8253 (pmm) REVERT: A 162 PHE cc_start: 0.9591 (m-80) cc_final: 0.9185 (m-80) REVERT: B 39 ASN cc_start: 0.9111 (t0) cc_final: 0.8802 (t0) REVERT: B 84 TYR cc_start: 0.8790 (m-80) cc_final: 0.8382 (m-80) REVERT: B 99 TYR cc_start: 0.8927 (t80) cc_final: 0.7407 (t80) REVERT: B 108 LEU cc_start: 0.9512 (pt) cc_final: 0.9281 (mt) REVERT: B 120 MET cc_start: 0.7699 (ppp) cc_final: 0.7479 (ppp) REVERT: B 158 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8571 (mt-10) REVERT: C 39 ASN cc_start: 0.8791 (t0) cc_final: 0.8495 (t0) REVERT: C 51 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8632 (tm-30) REVERT: C 52 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8733 (mm-40) REVERT: C 120 MET cc_start: 0.6635 (ppp) cc_final: 0.6097 (ppp) REVERT: C 134 PHE cc_start: 0.8441 (m-80) cc_final: 0.8088 (m-10) REVERT: D 39 ASN cc_start: 0.8831 (t0) cc_final: 0.8164 (t0) REVERT: D 89 MET cc_start: 0.9235 (mtp) cc_final: 0.8985 (mtp) REVERT: D 94 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.8864 (tppt) REVERT: D 134 PHE cc_start: 0.8634 (m-80) cc_final: 0.8319 (m-10) REVERT: D 142 ASP cc_start: 0.9223 (p0) cc_final: 0.8992 (p0) REVERT: D 156 GLU cc_start: 0.9102 (pt0) cc_final: 0.8878 (pt0) REVERT: E 17 TYR cc_start: 0.8960 (t80) cc_final: 0.8575 (t80) REVERT: E 21 ILE cc_start: 0.9074 (mt) cc_final: 0.8745 (mt) REVERT: E 89 MET cc_start: 0.9458 (mtm) cc_final: 0.8986 (mtm) REVERT: E 99 TYR cc_start: 0.8991 (t80) cc_final: 0.8659 (t80) REVERT: E 135 ILE cc_start: 0.8250 (mm) cc_final: 0.8043 (tp) REVERT: E 162 PHE cc_start: 0.9558 (m-80) cc_final: 0.9316 (m-80) REVERT: F 27 THR cc_start: 0.8634 (m) cc_final: 0.8410 (m) REVERT: F 39 ASN cc_start: 0.9101 (t0) cc_final: 0.8702 (t0) REVERT: F 48 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8258 (ttm110) REVERT: F 51 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8826 (tm-30) REVERT: F 52 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8871 (mm-40) REVERT: F 55 TYR cc_start: 0.9130 (t80) cc_final: 0.8875 (t80) REVERT: F 134 PHE cc_start: 0.8633 (m-80) cc_final: 0.8411 (m-10) REVERT: F 162 PHE cc_start: 0.9450 (m-80) cc_final: 0.9125 (m-80) REVERT: G 27 THR cc_start: 0.9036 (m) cc_final: 0.8645 (p) REVERT: G 36 ILE cc_start: 0.9583 (mm) cc_final: 0.9265 (pt) REVERT: G 84 TYR cc_start: 0.8860 (m-80) cc_final: 0.8313 (m-80) REVERT: G 89 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9080 (ttp) REVERT: G 96 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9514 (pp) REVERT: G 99 TYR cc_start: 0.9173 (t80) cc_final: 0.8895 (t80) REVERT: G 111 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9356 (tp) REVERT: G 144 LYS cc_start: 0.9082 (tppt) cc_final: 0.8833 (tppt) REVERT: G 162 PHE cc_start: 0.9605 (m-80) cc_final: 0.8966 (m-80) REVERT: H 43 MET cc_start: 0.9342 (mmm) cc_final: 0.9141 (mmm) REVERT: H 48 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8531 (ttm110) REVERT: H 89 MET cc_start: 0.9370 (mtt) cc_final: 0.9025 (mtm) REVERT: H 113 HIS cc_start: 0.9215 (m90) cc_final: 0.8752 (m-70) REVERT: H 120 MET cc_start: 0.7611 (ppp) cc_final: 0.7210 (ppp) REVERT: H 134 PHE cc_start: 0.8447 (m-80) cc_final: 0.8024 (m-10) REVERT: H 140 ARG cc_start: 0.8810 (ttp-110) cc_final: 0.8516 (ttp-110) REVERT: H 162 PHE cc_start: 0.9560 (m-80) cc_final: 0.9357 (m-80) REVERT: I 39 ASN cc_start: 0.9137 (t0) cc_final: 0.8678 (t0) REVERT: I 84 TYR cc_start: 0.8845 (m-80) cc_final: 0.8063 (m-80) REVERT: I 89 MET cc_start: 0.9549 (mtt) cc_final: 0.9300 (mtp) REVERT: I 110 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8659 (tt0) REVERT: I 144 LYS cc_start: 0.9106 (tppt) cc_final: 0.8749 (tppt) REVERT: I 162 PHE cc_start: 0.9566 (m-80) cc_final: 0.9209 (m-80) REVERT: J 39 ASN cc_start: 0.8619 (t0) cc_final: 0.8157 (t0) REVERT: J 43 MET cc_start: 0.9177 (mmm) cc_final: 0.8804 (mmm) REVERT: J 48 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8247 (tpp80) REVERT: J 53 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7717 (mm-30) REVERT: J 64 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8886 (p) REVERT: J 73 GLN cc_start: 0.9066 (pp30) cc_final: 0.8729 (pp30) REVERT: J 74 ILE cc_start: 0.9735 (mm) cc_final: 0.9534 (mm) REVERT: J 110 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8672 (tt0) REVERT: J 113 HIS cc_start: 0.8682 (m-70) cc_final: 0.8467 (m-70) REVERT: J 117 TRP cc_start: 0.8657 (t-100) cc_final: 0.8333 (t-100) REVERT: J 120 MET cc_start: 0.8383 (ppp) cc_final: 0.7980 (ppp) REVERT: J 134 PHE cc_start: 0.8595 (m-80) cc_final: 0.8251 (m-10) REVERT: J 140 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8281 (ttp-110) REVERT: J 162 PHE cc_start: 0.9360 (m-80) cc_final: 0.9108 (m-80) REVERT: K 21 ILE cc_start: 0.9190 (mt) cc_final: 0.8862 (mt) REVERT: K 39 ASN cc_start: 0.9033 (t0) cc_final: 0.8383 (t0) REVERT: K 44 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8387 (ptp-170) REVERT: K 73 GLN cc_start: 0.8914 (pp30) cc_final: 0.8536 (pp30) REVERT: K 74 ILE cc_start: 0.9630 (mm) cc_final: 0.9347 (mm) REVERT: K 78 TYR cc_start: 0.8804 (m-10) cc_final: 0.7954 (m-10) REVERT: K 84 TYR cc_start: 0.8931 (m-80) cc_final: 0.8195 (m-80) REVERT: K 89 MET cc_start: 0.9594 (mtt) cc_final: 0.9289 (mtm) REVERT: K 110 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8531 (mt-10) REVERT: K 134 PHE cc_start: 0.8637 (m-80) cc_final: 0.8320 (m-10) REVERT: K 140 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8432 (ttp-110) REVERT: K 144 LYS cc_start: 0.9216 (tppt) cc_final: 0.8722 (tppt) REVERT: L 43 MET cc_start: 0.9063 (mmm) cc_final: 0.8805 (mmm) REVERT: L 113 HIS cc_start: 0.8904 (m-70) cc_final: 0.8675 (m-70) REVERT: L 134 PHE cc_start: 0.8786 (m-80) cc_final: 0.8484 (m-10) REVERT: L 144 LYS cc_start: 0.9008 (tppt) cc_final: 0.8733 (tppt) REVERT: L 162 PHE cc_start: 0.9502 (m-80) cc_final: 0.9100 (m-80) REVERT: M 20 ARG cc_start: 0.9216 (mmm160) cc_final: 0.8870 (mmt180) REVERT: M 21 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8592 (mt) REVERT: M 36 ILE cc_start: 0.9732 (mm) cc_final: 0.9365 (mm) REVERT: M 39 ASN cc_start: 0.9050 (t0) cc_final: 0.8428 (t0) REVERT: M 43 MET cc_start: 0.9272 (mmm) cc_final: 0.9039 (mmm) REVERT: M 51 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8831 (tm-30) REVERT: M 52 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8829 (mm-40) REVERT: M 162 PHE cc_start: 0.9546 (m-80) cc_final: 0.9341 (m-80) REVERT: N 39 ASN cc_start: 0.8723 (t0) cc_final: 0.8042 (t0) REVERT: N 43 MET cc_start: 0.9281 (mmm) cc_final: 0.8915 (mmm) REVERT: N 48 ARG cc_start: 0.8971 (ttm-80) cc_final: 0.8426 (ttm110) REVERT: N 89 MET cc_start: 0.9556 (mtt) cc_final: 0.9281 (mtp) REVERT: N 162 PHE cc_start: 0.9273 (m-80) cc_final: 0.9061 (m-80) REVERT: P 39 ASN cc_start: 0.8845 (t0) cc_final: 0.8365 (t0) REVERT: P 48 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8480 (tpp80) REVERT: P 99 TYR cc_start: 0.9272 (t80) cc_final: 0.9024 (t80) REVERT: P 150 MET cc_start: 0.8915 (mpp) cc_final: 0.8428 (pmm) REVERT: P 162 PHE cc_start: 0.9482 (m-80) cc_final: 0.9279 (m-80) REVERT: R 48 ARG cc_start: 0.9174 (tpp80) cc_final: 0.8793 (tpp80) REVERT: R 89 MET cc_start: 0.9363 (mtp) cc_final: 0.8969 (ptm) REVERT: R 140 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8030 (mtm110) REVERT: R 162 PHE cc_start: 0.9208 (m-80) cc_final: 0.8782 (m-80) REVERT: T 51 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8772 (tm-30) REVERT: T 89 MET cc_start: 0.9276 (mtm) cc_final: 0.8640 (mtm) REVERT: T 99 TYR cc_start: 0.8487 (t80) cc_final: 0.8203 (t80) REVERT: T 110 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8792 (tt0) REVERT: T 162 PHE cc_start: 0.9242 (m-80) cc_final: 0.8581 (m-80) REVERT: a 121 GLU cc_start: 0.9120 (pm20) cc_final: 0.8851 (pm20) REVERT: a 152 ASP cc_start: 0.9387 (m-30) cc_final: 0.9173 (m-30) REVERT: b 113 MET cc_start: 0.8837 (tmm) cc_final: 0.8416 (tmm) REVERT: b 125 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8927 (pm20) REVERT: b 127 LYS cc_start: 0.9222 (ptpp) cc_final: 0.8878 (ptpp) REVERT: b 158 MET cc_start: 0.9234 (tpp) cc_final: 0.8869 (tpp) REVERT: b 170 MET cc_start: 0.8424 (mtm) cc_final: 0.8212 (mmm) REVERT: c 38 GLN cc_start: 0.9296 (tp40) cc_final: 0.9072 (tp40) REVERT: d 126 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9162 (tp) REVERT: e 24 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9442 (mm) REVERT: e 27 ILE cc_start: 0.9545 (mm) cc_final: 0.9228 (tp) REVERT: e 38 GLN cc_start: 0.9242 (tp40) cc_final: 0.8925 (tp-100) REVERT: e 39 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8690 (mm-40) REVERT: e 59 MET cc_start: 0.9267 (mmm) cc_final: 0.9061 (mmm) REVERT: e 113 MET cc_start: 0.8988 (tmm) cc_final: 0.8524 (tmm) REVERT: e 125 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9156 (mp10) REVERT: e 127 LYS cc_start: 0.9534 (ptpp) cc_final: 0.9177 (ptpp) REVERT: e 158 MET cc_start: 0.9455 (tpp) cc_final: 0.9036 (tpp) REVERT: f 44 MET cc_start: 0.8926 (ttm) cc_final: 0.8621 (ttm) REVERT: g 11 ASP cc_start: 0.8383 (m-30) cc_final: 0.7992 (m-30) REVERT: g 127 LYS cc_start: 0.9366 (pttm) cc_final: 0.9090 (ptpp) REVERT: g 152 ASP cc_start: 0.9374 (m-30) cc_final: 0.9083 (m-30) REVERT: g 158 MET cc_start: 0.9424 (tpp) cc_final: 0.9129 (tpp) REVERT: g 174 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9046 (p) REVERT: g 190 MET cc_start: 0.8348 (pmm) cc_final: 0.8092 (pmm) REVERT: g 191 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8893 (tm-30) REVERT: h 11 ASP cc_start: 0.8020 (m-30) cc_final: 0.7780 (m-30) REVERT: h 158 MET cc_start: 0.9065 (tpp) cc_final: 0.8708 (tpp) REVERT: i 158 MET cc_start: 0.9235 (tpp) cc_final: 0.8887 (tpp) REVERT: j 32 MET cc_start: 0.8834 (mmp) cc_final: 0.8536 (mmm) REVERT: j 82 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9429 (tp) REVERT: j 126 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8957 (tp) REVERT: k 58 LYS cc_start: 0.9408 (ttmm) cc_final: 0.9120 (tptp) REVERT: k 158 MET cc_start: 0.8898 (tpp) cc_final: 0.8687 (tpp) REVERT: k 199 ASP cc_start: 0.9347 (p0) cc_final: 0.8967 (p0) REVERT: l 27 ILE cc_start: 0.9352 (mm) cc_final: 0.9082 (mt) REVERT: l 96 GLU cc_start: 0.8907 (mp0) cc_final: 0.8410 (mp0) REVERT: m 59 MET cc_start: 0.9158 (mmm) cc_final: 0.8842 (mmp) REVERT: m 96 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8603 (mt-10) REVERT: m 127 LYS cc_start: 0.9562 (pttp) cc_final: 0.9287 (pttp) REVERT: m 158 MET cc_start: 0.9242 (tpp) cc_final: 0.8911 (tpp) REVERT: m 170 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: m 171 LYS cc_start: 0.9119 (pttp) cc_final: 0.8732 (tppt) REVERT: m 194 TYR cc_start: 0.9141 (m-80) cc_final: 0.8885 (m-80) REVERT: m 198 GLU cc_start: 0.9215 (pt0) cc_final: 0.8920 (tp30) REVERT: n 44 MET cc_start: 0.8606 (mmm) cc_final: 0.8140 (mmm) REVERT: n 59 MET cc_start: 0.8907 (mmm) cc_final: 0.8596 (mmm) REVERT: n 113 MET cc_start: 0.8872 (tpp) cc_final: 0.8542 (tpp) REVERT: n 116 LYS cc_start: 0.9659 (mtmt) cc_final: 0.9307 (mtmm) REVERT: n 127 LYS cc_start: 0.9586 (pttp) cc_final: 0.9283 (ptpp) REVERT: n 135 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7276 (mp0) REVERT: p 38 GLN cc_start: 0.9207 (tp40) cc_final: 0.8805 (tp40) REVERT: p 127 LYS cc_start: 0.9541 (pttp) cc_final: 0.9037 (ptpt) REVERT: p 187 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.5938 (t80) REVERT: r 44 MET cc_start: 0.8721 (tpp) cc_final: 0.8350 (tpt) REVERT: r 121 GLU cc_start: 0.9498 (mp0) cc_final: 0.9239 (pm20) REVERT: r 171 LYS cc_start: 0.9254 (ptpp) cc_final: 0.8803 (tptt) REVERT: r 199 ASP cc_start: 0.9137 (p0) cc_final: 0.8862 (p0) REVERT: t 21 LYS cc_start: 0.9514 (mttt) cc_final: 0.8870 (tmtt) REVERT: t 116 LYS cc_start: 0.9608 (ptmt) cc_final: 0.9395 (ptpp) REVERT: t 127 LYS cc_start: 0.9411 (pttm) cc_final: 0.9169 (ptpp) REVERT: t 152 ASP cc_start: 0.9314 (m-30) cc_final: 0.9098 (m-30) REVERT: t 194 TYR cc_start: 0.9014 (m-80) cc_final: 0.8711 (m-80) REVERT: t 199 ASP cc_start: 0.9287 (p0) cc_final: 0.8989 (p0) outliers start: 144 outliers final: 118 residues processed: 1299 average time/residue: 0.5952 time to fit residues: 1251.9107 Evaluate side-chains 1275 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1144 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 170 MET Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain b residue 14 ASN Chi-restraints excluded: chain b residue 82 LEU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 140 VAL Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 180 HIS Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain c residue 82 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 180 HIS Chi-restraints excluded: chain d residue 14 ASN Chi-restraints excluded: chain d residue 126 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 153 ASN Chi-restraints excluded: chain e residue 165 TYR Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 180 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain h residue 163 ASN Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain h residue 198 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 148 VAL Chi-restraints excluded: chain i residue 180 HIS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain j residue 168 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain k residue 129 LEU Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 144 HIS Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 170 MET Chi-restraints excluded: chain k residue 180 HIS Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 153 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 HIS Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 170 MET Chi-restraints excluded: chain m residue 180 HIS Chi-restraints excluded: chain m residue 200 ILE Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain n residue 170 MET Chi-restraints excluded: chain p residue 14 ASN Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain p residue 140 VAL Chi-restraints excluded: chain p residue 148 VAL Chi-restraints excluded: chain p residue 187 PHE Chi-restraints excluded: chain p residue 188 SER Chi-restraints excluded: chain r residue 14 ASN Chi-restraints excluded: chain r residue 148 VAL Chi-restraints excluded: chain t residue 97 THR Chi-restraints excluded: chain t residue 130 VAL Chi-restraints excluded: chain t residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 310 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 540 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 467 optimal weight: 8.9990 chunk 74 optimal weight: 40.0000 chunk 140 optimal weight: 10.0000 chunk 507 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 chunk 521 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 GLN ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 HIS d 39 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 180 HIS k 144 HIS n 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.047085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.039546 restraints weight = 404595.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040665 restraints weight = 211830.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.041379 restraints weight = 142411.492| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 58327 Z= 0.293 Angle : 0.959 16.131 81125 Z= 0.517 Chirality : 0.046 0.212 9340 Planarity : 0.005 0.062 8642 Dihedral : 17.221 70.432 11967 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.88 % Allowed : 28.79 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 5950 helix: 0.25 (0.08), residues: 4335 sheet: 0.26 (0.34), residues: 204 loop : -2.31 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 117 HIS 0.022 0.001 HIS h 180 PHE 0.021 0.002 PHE M 134 TYR 0.032 0.002 TYR c 45 ARG 0.014 0.001 ARG L 15 =============================================================================== Job complete usr+sys time: 18198.97 seconds wall clock time: 313 minutes 23.49 seconds (18803.49 seconds total)