Starting phenix.real_space_refine on Fri Dec 15 23:56:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2023/7v66_31736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2023/7v66_31736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2023/7v66_31736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2023/7v66_31736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2023/7v66_31736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2023/7v66_31736.pdb" } resolution = 1.89 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= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20904 2.51 5 N 5808 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 5": "NH1" <-> "NH2" Residue "U GLU 163": "OE1" <-> "OE2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "K ARG 5": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "X GLU 163": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33216 Number of models: 1 Model: "" Number of chains: 24 Chain: "U" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Q" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "V" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "W" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "X" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 18.35, per 1000 atoms: 0.55 Number of scatterers: 33216 At special positions: 0 Unit cell: (130.295, 130.295, 130.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 6336 8.00 N 5808 7.00 C 20904 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 - 3.50 Amino acid : False - 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: 14.52 Conformation dependent library (CDL) restraints added in 6.4 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'U' and resid 9 through 38 Processing helix chain 'U' and resid 44 through 72 Processing helix chain 'U' and resid 91 through 120 Processing helix chain 'U' and resid 122 through 133 Processing helix chain 'U' and resid 133 through 154 Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.809A pdb=" N GLU U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 154 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 38 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 91 through 120 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 133 through 154 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 154 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 154 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 38 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 154 Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.809A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 38 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 154 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 38 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 154 Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 38 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 154 Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 38 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 154 Processing helix chain 'I' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 38 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 154 Processing helix chain 'J' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 38 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 154 Processing helix chain 'K' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 38 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 154 Processing helix chain 'L' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 38 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 154 Processing helix chain 'M' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU M 163 " --> pdb=" O SER M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 154 Processing helix chain 'N' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU N 163 " --> pdb=" O SER N 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 38 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 154 Processing helix chain 'O' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU O 163 " --> pdb=" O SER O 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 38 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 154 Processing helix chain 'P' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 38 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 154 Processing helix chain 'Q' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 38 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 154 Processing helix chain 'R' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 38 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 154 Processing helix chain 'S' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU S 163 " --> pdb=" O SER S 159 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 38 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 154 Processing helix chain 'T' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU T 163 " --> pdb=" O SER T 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 38 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 154 Processing helix chain 'V' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU V 163 " --> pdb=" O SER V 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 38 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 154 Processing helix chain 'W' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU W 163 " --> pdb=" O SER W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 38 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 154 Processing helix chain 'X' and resid 159 through 170 removed outlier: 3.806A pdb=" N GLU X 163 " --> pdb=" O SER X 159 " (cutoff:3.500A) 2637 hydrogen bonds defined for protein. 7911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.99 Time building geometry restraints manager: 15.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10606 1.34 - 1.46: 4943 1.46 - 1.57: 18099 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 33912 Sorted by residual: bond pdb=" C ALA M 156 " pdb=" N PRO M 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA V 156 " pdb=" N PRO V 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA T 156 " pdb=" N PRO T 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA A 156 " pdb=" N PRO A 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA X 156 " pdb=" N PRO X 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 ... (remaining 33907 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.33: 653 106.33 - 113.20: 17808 113.20 - 120.07: 12204 120.07 - 126.95: 14719 126.95 - 133.82: 408 Bond angle restraints: 45792 Sorted by residual: angle pdb=" C ALA W 156 " pdb=" N PRO W 157 " pdb=" CA PRO W 157 " ideal model delta sigma weight residual 119.84 129.45 -9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" N GLU B 90 " pdb=" CA GLU B 90 " pdb=" C GLU B 90 " ideal model delta sigma weight residual 110.80 123.65 -12.85 2.13e+00 2.20e-01 3.64e+01 angle pdb=" N LYS S 45 " pdb=" CA LYS S 45 " pdb=" C LYS S 45 " ideal model delta sigma weight residual 111.28 117.33 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N THR U 131 " pdb=" CA THR U 131 " pdb=" C THR U 131 " ideal model delta sigma weight residual 111.82 117.22 -5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N THR B 131 " pdb=" CA THR B 131 " pdb=" C THR B 131 " ideal model delta sigma weight residual 111.82 117.22 -5.40 1.16e+00 7.43e-01 2.16e+01 ... (remaining 45787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 19381 17.57 - 35.14: 609 35.14 - 52.71: 287 52.71 - 70.28: 50 70.28 - 87.84: 25 Dihedral angle restraints: 20352 sinusoidal: 8112 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP H 89 " pdb=" C TRP H 89 " pdb=" N GLU H 90 " pdb=" CA GLU H 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP A 89 " pdb=" C TRP A 89 " pdb=" N GLU A 90 " pdb=" CA GLU A 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP T 89 " pdb=" C TRP T 89 " pdb=" N GLU T 90 " pdb=" CA GLU T 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 20349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4699 0.118 - 0.236: 154 0.236 - 0.354: 19 0.354 - 0.472: 1 0.472 - 0.590: 23 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CG LEU K 151 " pdb=" CB LEU K 151 " pdb=" CD1 LEU K 151 " pdb=" CD2 LEU K 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CG LEU I 151 " pdb=" CB LEU I 151 " pdb=" CD1 LEU I 151 " pdb=" CD2 LEU I 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CG LEU J 151 " pdb=" CB LEU J 151 " pdb=" CD1 LEU J 151 " pdb=" CD2 LEU J 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 4893 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR H 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR H 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 28 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR A 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 28 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR B 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 92 2.52 - 3.12: 24800 3.12 - 3.71: 56422 3.71 - 4.31: 80819 4.31 - 4.90: 131955 Nonbonded interactions: 294088 Sorted by model distance: nonbonded pdb=" O GLY D 155 " pdb=" OG SER D 159 " model vdw 1.929 2.440 nonbonded pdb=" O GLY W 155 " pdb=" OG SER W 159 " model vdw 2.206 2.440 nonbonded pdb=" OD2 ASP B 40 " pdb=" OG SER D 2 " model vdw 2.305 2.440 nonbonded pdb=" OG SER Q 2 " pdb=" OD2 ASP W 40 " model vdw 2.305 2.440 nonbonded pdb=" OD2 ASP O 40 " pdb=" OG SER R 2 " model vdw 2.305 2.440 ... (remaining 294083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 individual isotropic 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.280 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 87.860 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.290 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:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0489 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 : 0.006 0.059 33912 Z= 0.372 Angle : 1.018 12.850 45792 Z= 0.581 Chirality : 0.067 0.590 4896 Planarity : 0.006 0.026 6024 Dihedral : 12.145 87.844 12432 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 2.07 % Allowed : 2.73 % Favored : 95.20 % 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: 1.97 (0.13), residues: 4080 helix: 1.80 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.65 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 89 HIS 0.026 0.005 HIS M 147 PHE 0.016 0.004 PHE N 37 TYR 0.063 0.006 TYR A 28 ARG 0.009 0.003 ARG O 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 288 time to evaluate : 3.827 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 outliers start: 72 outliers final: 0 residues processed: 360 average time/residue: 1.1362 time to fit residues: 511.7449 Evaluate side-chains 240 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN U 94 ASN U 108 GLN U 135 ASN U 150 ASN A 7 ASN A 19 GLN A 94 ASN A 108 GLN A 135 ASN A 150 ASN B 7 ASN B 10 GLN B 19 GLN B 94 ASN B 135 ASN B 150 ASN C 7 ASN C 19 GLN C 94 ASN C 108 GLN C 150 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 94 ASN D 108 GLN D 150 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 94 ASN E 108 GLN E 150 ASN F 7 ASN F 19 GLN F 94 ASN F 150 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN G 94 ASN G 108 GLN G 150 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 94 ASN H 108 GLN H 150 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 94 ASN I 108 GLN I 135 ASN I 150 ASN J 7 ASN J 19 GLN J 79 GLN J 94 ASN J 108 GLN J 150 ASN K 7 ASN K 19 GLN K 94 ASN K 108 GLN K 150 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 94 ASN L 108 GLN L 150 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN M 94 ASN M 108 GLN M 150 ASN N 7 ASN N 19 GLN N 94 ASN N 150 ASN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN O 94 ASN O 108 GLN O 150 ASN ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN P 94 ASN P 108 GLN P 150 ASN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 94 ASN Q 108 GLN Q 150 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN R 94 ASN R 108 GLN R 135 ASN R 150 ASN S 7 ASN S 19 GLN S 94 ASN S 108 GLN S 150 ASN T 7 ASN T 19 GLN T 94 ASN T 108 GLN T 150 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN V 94 ASN V 108 GLN V 150 ASN W 7 ASN W 19 GLN W 94 ASN W 108 GLN W 150 ASN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN X 94 ASN X 108 GLN X 150 ASN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1005 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33912 Z= 0.232 Angle : 0.663 9.344 45792 Z= 0.354 Chirality : 0.043 0.183 4896 Planarity : 0.004 0.025 6024 Dihedral : 4.785 21.074 4464 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.84 % Allowed : 6.06 % Favored : 91.09 % 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: 3.06 (0.13), residues: 4080 helix: 2.68 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.85 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP U 89 HIS 0.006 0.002 HIS C 61 PHE 0.007 0.002 PHE S 47 TYR 0.031 0.003 TYR Q 164 ARG 0.004 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 204 time to evaluate : 3.342 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 outliers start: 99 outliers final: 14 residues processed: 269 average time/residue: 1.0784 time to fit residues: 370.4274 Evaluate side-chains 206 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 3.534 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 4 residues processed: 11 average time/residue: 0.5382 time to fit residues: 14.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 0.6980 chunk 330 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN U 54 GLN U 132 HIS U 135 ASN U 137 GLN A 19 GLN A 54 GLN A 135 ASN A 137 GLN B 19 GLN B 54 GLN B 108 GLN B 132 HIS B 135 ASN C 54 GLN C 132 HIS D 7 ASN D 19 GLN D 54 GLN D 132 HIS E 7 ASN E 19 GLN E 54 GLN E 132 HIS E 137 GLN F 19 GLN F 54 GLN F 108 GLN F 132 HIS F 137 GLN G 7 ASN G 19 GLN G 54 GLN G 132 HIS G 137 GLN H 7 ASN H 19 GLN H 54 GLN H 132 HIS I 7 ASN I 19 GLN I 54 GLN I 132 HIS I 135 ASN I 137 GLN J 54 GLN J 132 HIS J 137 GLN K 19 GLN K 54 GLN K 132 HIS K 137 GLN L 7 ASN L 19 GLN L 54 GLN L 132 HIS ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN M 54 GLN M 132 HIS N 19 GLN N 54 GLN N 108 GLN N 132 HIS O 7 ASN O 19 GLN O 54 GLN O 132 HIS O 137 GLN P 7 ASN P 19 GLN P 54 GLN P 132 HIS P 137 GLN Q 7 ASN Q 54 GLN Q 132 HIS R 7 ASN R 19 GLN R 54 GLN R 132 HIS R 135 ASN R 137 GLN S 19 GLN S 54 GLN S 132 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN T 54 GLN ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 137 GLN V 7 ASN V 19 GLN V 54 GLN V 132 HIS V 137 GLN W 19 GLN W 54 GLN W 132 HIS W 137 GLN X 7 ASN X 54 GLN X 132 HIS X 137 GLN Total number of N/Q/H flips: 101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1290 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33912 Z= 0.283 Angle : 0.753 8.809 45792 Z= 0.396 Chirality : 0.043 0.177 4896 Planarity : 0.005 0.034 6024 Dihedral : 5.232 20.942 4464 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.42 % Allowed : 5.55 % Favored : 91.03 % 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: 1.82 (0.13), residues: 4080 helix: 1.87 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 89 HIS 0.009 0.002 HIS T 132 PHE 0.010 0.002 PHE N 128 TYR 0.027 0.003 TYR O 164 ARG 0.004 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 218 time to evaluate : 3.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 49 residues processed: 268 average time/residue: 1.0960 time to fit residues: 373.2217 Evaluate side-chains 248 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 3.359 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 23 residues processed: 26 average time/residue: 0.4202 time to fit residues: 23.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN A 19 GLN A 132 HIS B 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 137 GLN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN N 19 GLN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN R 19 GLN S 19 GLN T 19 GLN V 19 GLN W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1286 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33912 Z= 0.212 Angle : 0.643 14.506 45792 Z= 0.340 Chirality : 0.040 0.174 4896 Planarity : 0.004 0.036 6024 Dihedral : 4.790 18.882 4464 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.28 % Allowed : 6.67 % Favored : 90.06 % 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: 2.31 (0.13), residues: 4080 helix: 2.26 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP U 89 HIS 0.008 0.002 HIS P 61 PHE 0.017 0.002 PHE G 47 TYR 0.020 0.002 TYR K 164 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 203 time to evaluate : 3.602 Fit side-chains revert: symmetry clash outliers start: 114 outliers final: 52 residues processed: 256 average time/residue: 1.1160 time to fit residues: 362.2814 Evaluate side-chains 253 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 201 time to evaluate : 3.928 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 28 residues processed: 27 average time/residue: 0.5717 time to fit residues: 28.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 10.9990 chunk 201 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 150 ASN A 19 GLN B 19 GLN C 19 GLN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 19 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN N 19 GLN O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1275 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33912 Z= 0.181 Angle : 0.610 10.051 45792 Z= 0.313 Chirality : 0.038 0.168 4896 Planarity : 0.003 0.038 6024 Dihedral : 4.559 19.754 4464 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.45 % Allowed : 7.84 % Favored : 88.71 % 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: 2.66 (0.13), residues: 4080 helix: 2.51 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.18 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 89 HIS 0.008 0.001 HIS K 61 PHE 0.009 0.001 PHE G 47 TYR 0.022 0.002 TYR E 164 ARG 0.002 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 197 time to evaluate : 3.734 Fit side-chains revert: symmetry clash outliers start: 120 outliers final: 50 residues processed: 262 average time/residue: 1.0821 time to fit residues: 362.3736 Evaluate side-chains 222 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 172 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 27 residues processed: 25 average time/residue: 0.5243 time to fit residues: 25.9513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 327 optimal weight: 0.0770 chunk 182 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 0.2980 chunk 207 optimal weight: 6.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN B 19 GLN C 19 GLN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN K 3 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN N 3 GLN O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1212 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33912 Z= 0.152 Angle : 0.581 9.244 45792 Z= 0.293 Chirality : 0.037 0.162 4896 Planarity : 0.003 0.039 6024 Dihedral : 4.425 20.857 4464 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.59 % Allowed : 9.05 % Favored : 88.36 % 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: 3.25 (0.13), residues: 4080 helix: 2.92 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP W 89 HIS 0.005 0.001 HIS A 61 PHE 0.015 0.001 PHE W 47 TYR 0.019 0.002 TYR X 35 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 182 time to evaluate : 3.920 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 45 residues processed: 211 average time/residue: 1.3333 time to fit residues: 348.7013 Evaluate side-chains 224 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 26 residues processed: 20 average time/residue: 0.5231 time to fit residues: 21.8606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 9.9990 chunk 246 optimal weight: 0.5980 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 61 HIS C 19 GLN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 61 HIS ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 19 GLN J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 GLN R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1386 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33912 Z= 0.221 Angle : 0.663 10.512 45792 Z= 0.344 Chirality : 0.039 0.172 4896 Planarity : 0.004 0.040 6024 Dihedral : 4.698 20.680 4464 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.87 % Allowed : 10.00 % Favored : 87.13 % 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: 2.45 (0.13), residues: 4080 helix: 2.37 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.28 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 89 HIS 0.018 0.002 HIS F 61 PHE 0.011 0.002 PHE C 51 TYR 0.027 0.002 TYR V 164 ARG 0.004 0.000 ARG R 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 173 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 45 residues processed: 198 average time/residue: 1.3744 time to fit residues: 336.6796 Evaluate side-chains 218 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 3.468 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 23 residues processed: 22 average time/residue: 0.4895 time to fit residues: 22.3856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN J 19 GLN L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN N 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1294 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33912 Z= 0.174 Angle : 0.597 8.290 45792 Z= 0.306 Chirality : 0.037 0.164 4896 Planarity : 0.003 0.040 6024 Dihedral : 4.474 21.561 4464 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.01 % Allowed : 10.89 % Favored : 87.10 % 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: 2.82 (0.13), residues: 4080 helix: 2.62 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.09 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 89 HIS 0.020 0.001 HIS F 61 PHE 0.013 0.001 PHE C 47 TYR 0.023 0.002 TYR D 164 ARG 0.003 0.000 ARG X 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 172 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 39 residues processed: 196 average time/residue: 1.3803 time to fit residues: 331.5762 Evaluate side-chains 210 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 3.843 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 25 residues processed: 15 average time/residue: 0.6620 time to fit residues: 20.0856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 5.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 0.4980 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 0.0870 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1349 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33912 Z= 0.184 Angle : 0.631 9.433 45792 Z= 0.323 Chirality : 0.038 0.167 4896 Planarity : 0.003 0.041 6024 Dihedral : 4.465 21.066 4464 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.13 % Allowed : 10.63 % Favored : 87.24 % 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: 2.78 (0.13), residues: 4080 helix: 2.61 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.20 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 89 HIS 0.019 0.001 HIS F 61 PHE 0.009 0.001 PHE K 37 TYR 0.021 0.002 TYR C 30 ARG 0.002 0.000 ARG L 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 172 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 35 residues processed: 197 average time/residue: 1.3355 time to fit residues: 323.8739 Evaluate side-chains 207 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 10 average time/residue: 0.6200 time to fit residues: 14.2675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 0.0870 chunk 183 optimal weight: 0.4980 chunk 269 optimal weight: 0.9990 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 0.0020 chunk 323 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1203 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33912 Z= 0.139 Angle : 0.574 9.431 45792 Z= 0.289 Chirality : 0.036 0.158 4896 Planarity : 0.002 0.045 6024 Dihedral : 4.249 21.613 4464 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.35 % Allowed : 11.21 % Favored : 87.44 % 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: 3.37 (0.13), residues: 4080 helix: 3.07 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -1.05 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 89 HIS 0.015 0.001 HIS F 61 PHE 0.014 0.001 PHE U 47 TYR 0.021 0.001 TYR T 35 ARG 0.002 0.000 ARG O 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 3.741 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 36 residues processed: 233 average time/residue: 1.2471 time to fit residues: 362.5004 Evaluate side-chains 219 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 26 residues processed: 11 average time/residue: 0.5141 time to fit residues: 14.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.283109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.275410 restraints weight = 241987.452| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 3.87 r_work: 0.4441 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1397 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33912 Z= 0.251 Angle : 0.719 11.432 45792 Z= 0.371 Chirality : 0.040 0.170 4896 Planarity : 0.003 0.044 6024 Dihedral : 4.624 21.056 4464 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.38 % Allowed : 12.44 % Favored : 86.18 % 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: 2.56 (0.13), residues: 4080 helix: 2.46 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.33 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 89 HIS 0.010 0.001 HIS T 61 PHE 0.031 0.002 PHE S 51 TYR 0.025 0.002 TYR T 164 ARG 0.003 0.000 ARG K 152 =============================================================================== Job complete usr+sys time: 8188.63 seconds wall clock time: 149 minutes 23.07 seconds (8963.07 seconds total)