Starting phenix.real_space_refine on Sun Apr 14 12:01:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v05_26936/04_2024/7v05_26936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v05_26936/04_2024/7v05_26936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v05_26936/04_2024/7v05_26936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v05_26936/04_2024/7v05_26936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v05_26936/04_2024/7v05_26936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v05_26936/04_2024/7v05_26936.pdb" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.004 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 47382 atoms to isotropic. 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 154 5.16 5 C 29802 2.51 5 N 7936 2.21 5 O 9490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 47382 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 776 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 83} Chain: "I" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "m" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1689 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1640 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 18.96, per 1000 atoms: 0.40 Number of scatterers: 47382 At special positions: 0 Unit cell: (168.92, 169.95, 210.12, 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 154 16.00 O 9490 8.00 N 7936 7.00 C 29802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.04 Simple disulfide: pdb=" SG CYS a 133 " - pdb=" SG CYS a 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 88 " distance=2.03 Simple disulfide: pdb=" SG CYS b 133 " - pdb=" SG CYS b 193 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 23 " - pdb=" SG CYS c 88 " distance=2.04 Simple disulfide: pdb=" SG CYS c 133 " - pdb=" SG CYS c 193 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 133 " - pdb=" SG CYS d 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.04 Simple disulfide: pdb=" SG CYS e 133 " - pdb=" SG CYS e 193 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 133 " - pdb=" SG CYS f 193 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.03 Simple disulfide: pdb=" SG CYS g 133 " - pdb=" SG CYS g 193 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 88 " distance=2.03 Simple disulfide: pdb=" SG CYS h 133 " - pdb=" SG CYS h 193 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS i 23 " - pdb=" SG CYS i 88 " distance=2.03 Simple disulfide: pdb=" SG CYS i 133 " - pdb=" SG CYS i 193 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 140 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS j 23 " - pdb=" SG CYS j 88 " distance=2.03 Simple disulfide: pdb=" SG CYS j 133 " - pdb=" SG CYS j 193 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS k 23 " - pdb=" SG CYS k 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 133 " - pdb=" SG CYS k 193 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS l 133 " - pdb=" SG CYS l 193 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 133 " - pdb=" SG CYS m 193 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 196 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS n 133 " - pdb=" SG CYS n 193 " distance=2.04 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: 13.98 Conformation dependent library (CDL) restraints added in 6.7 seconds 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11506 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 154 sheets defined 9.4% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'a' and resid 79 through 83 removed outlier: 3.508A pdb=" N PHE a 83 " --> pdb=" O PRO a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 127 Processing helix chain 'a' and resid 182 through 187 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'b' and resid 79 through 83 removed outlier: 3.603A pdb=" N PHE b 83 " --> pdb=" O PRO b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 127 Processing helix chain 'b' and resid 182 through 187 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'c' and resid 79 through 83 removed outlier: 3.604A pdb=" N PHE c 83 " --> pdb=" O PRO c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 127 Processing helix chain 'c' and resid 182 through 187 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'd' and resid 79 through 83 removed outlier: 3.564A pdb=" N PHE d 83 " --> pdb=" O PRO d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 127 Processing helix chain 'd' and resid 182 through 187 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 156 through 158 No H-bonds generated for 'chain 'E' and resid 156 through 158' Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'e' and resid 79 through 83 removed outlier: 3.568A pdb=" N PHE e 83 " --> pdb=" O PRO e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 127 Processing helix chain 'e' and resid 182 through 187 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'f' and resid 79 through 83 removed outlier: 3.617A pdb=" N PHE f 83 " --> pdb=" O PRO f 80 " (cutoff:3.500A) Processing helix chain 'f' and resid 120 through 127 Processing helix chain 'f' and resid 182 through 187 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 127 through 129 No H-bonds generated for 'chain 'G' and resid 127 through 129' Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'g' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE g 83 " --> pdb=" O PRO g 80 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 127 Processing helix chain 'g' and resid 182 through 187 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'h' and resid 79 through 83 removed outlier: 3.591A pdb=" N PHE h 83 " --> pdb=" O PRO h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 120 through 127 Processing helix chain 'h' and resid 182 through 187 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'I' and resid 201 through 204 Processing helix chain 'i' and resid 79 through 83 removed outlier: 3.600A pdb=" N PHE i 83 " --> pdb=" O PRO i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 127 Processing helix chain 'i' and resid 182 through 187 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 127 through 129 No H-bonds generated for 'chain 'J' and resid 127 through 129' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 187 through 189 No H-bonds generated for 'chain 'J' and resid 187 through 189' Processing helix chain 'J' and resid 201 through 204 Processing helix chain 'j' and resid 79 through 83 removed outlier: 3.532A pdb=" N PHE j 83 " --> pdb=" O PRO j 80 " (cutoff:3.500A) Processing helix chain 'j' and resid 120 through 127 Processing helix chain 'j' and resid 182 through 187 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 127 through 129 No H-bonds generated for 'chain 'K' and resid 127 through 129' Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'k' and resid 79 through 83 removed outlier: 3.589A pdb=" N PHE k 83 " --> pdb=" O PRO k 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 120 through 127 Processing helix chain 'k' and resid 182 through 187 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 127 through 129 No H-bonds generated for 'chain 'L' and resid 127 through 129' Processing helix chain 'L' and resid 156 through 158 No H-bonds generated for 'chain 'L' and resid 156 through 158' Processing helix chain 'L' and resid 187 through 189 No H-bonds generated for 'chain 'L' and resid 187 through 189' Processing helix chain 'L' and resid 201 through 204 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.603A pdb=" N PHE l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 120 through 127 Processing helix chain 'l' and resid 182 through 187 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 127 through 129 No H-bonds generated for 'chain 'M' and resid 127 through 129' Processing helix chain 'M' and resid 156 through 158 No H-bonds generated for 'chain 'M' and resid 156 through 158' Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 201 through 204 Processing helix chain 'm' and resid 79 through 83 removed outlier: 3.573A pdb=" N PHE m 83 " --> pdb=" O PRO m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 120 through 127 Processing helix chain 'm' and resid 182 through 187 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 127 through 129 No H-bonds generated for 'chain 'N' and resid 127 through 129' Processing helix chain 'N' and resid 156 through 158 No H-bonds generated for 'chain 'N' and resid 156 through 158' Processing helix chain 'N' and resid 187 through 189 No H-bonds generated for 'chain 'N' and resid 187 through 189' Processing helix chain 'N' and resid 201 through 204 Processing helix chain 'n' and resid 79 through 83 removed outlier: 3.580A pdb=" N PHE n 83 " --> pdb=" O PRO n 80 " (cutoff:3.500A) Processing helix chain 'n' and resid 120 through 127 Processing helix chain 'n' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.727A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.747A pdb=" N VAL A 102 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 124 removed outlier: 6.113A pdb=" N TYR A 176 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 132 removed outlier: 6.113A pdb=" N TYR A 176 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 154 removed outlier: 4.401A pdb=" N TYR A 194 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 4 through 7 removed outlier: 3.884A pdb=" N GLU a 70 " --> pdb=" O SER a 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 10 through 13 removed outlier: 6.623A pdb=" N LEU a 33 " --> pdb=" O TYR a 49 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR a 49 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP a 35 " --> pdb=" O LEU a 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 10 through 13 removed outlier: 3.632A pdb=" N THR a 96 " --> pdb=" O GLN a 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 113 through 117 removed outlier: 6.158A pdb=" N TYR a 172 " --> pdb=" O ASN a 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.787A pdb=" N MET B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.776A pdb=" N VAL B 102 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 120 through 124 removed outlier: 5.359A pdb=" N ALA B 137 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 184 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY B 139 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL B 182 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU B 141 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER B 180 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS B 143 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 178 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 131 through 132 removed outlier: 5.359A pdb=" N ALA B 137 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 184 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY B 139 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL B 182 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU B 141 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER B 180 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS B 143 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 178 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 151 through 154 Processing sheet with id=AB9, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.855A pdb=" N GLU b 70 " --> pdb=" O SER b 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.474A pdb=" N LEU b 33 " --> pdb=" O TYR b 49 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR b 49 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP b 35 " --> pdb=" O LEU b 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 10 through 13 removed outlier: 3.539A pdb=" N THR b 96 " --> pdb=" O GLN b 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 113 through 117 removed outlier: 5.893A pdb=" N TYR b 172 " --> pdb=" O ASN b 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 152 through 153 Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.562A pdb=" N VAL C 12 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.562A pdb=" N VAL C 12 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 102 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.315A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.566A pdb=" N THR C 135 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AD2, first strand: chain 'c' and resid 4 through 7 removed outlier: 3.893A pdb=" N GLU c 70 " --> pdb=" O SER c 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 10 through 13 removed outlier: 6.524A pdb=" N LEU c 33 " --> pdb=" O TYR c 49 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR c 49 " --> pdb=" O LEU c 33 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP c 35 " --> pdb=" O LEU c 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 10 through 13 removed outlier: 3.547A pdb=" N THR c 96 " --> pdb=" O GLN c 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 113 through 117 removed outlier: 5.858A pdb=" N TYR c 172 " --> pdb=" O ASN c 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 152 through 153 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.739A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.791A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.042A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 131 through 132 removed outlier: 6.042A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AE4, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.911A pdb=" N GLU d 70 " --> pdb=" O SER d 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 10 through 13 removed outlier: 6.591A pdb=" N LEU d 33 " --> pdb=" O TYR d 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR d 49 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP d 35 " --> pdb=" O LEU d 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 10 through 13 removed outlier: 3.512A pdb=" N THR d 96 " --> pdb=" O GLN d 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 113 through 117 removed outlier: 5.934A pdb=" N TYR d 172 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 152 through 153 Processing sheet with id=AE9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.738A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.753A pdb=" N VAL E 102 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 120 through 124 removed outlier: 6.066A pdb=" N TYR E 176 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.663A pdb=" N THR E 135 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR E 176 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 151 through 154 Processing sheet with id=AF6, first strand: chain 'e' and resid 4 through 7 removed outlier: 3.879A pdb=" N GLU e 70 " --> pdb=" O SER e 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 10 through 13 removed outlier: 6.500A pdb=" N LEU e 33 " --> pdb=" O TYR e 49 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR e 49 " --> pdb=" O LEU e 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP e 35 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 10 through 13 removed outlier: 3.581A pdb=" N THR e 96 " --> pdb=" O GLN e 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'e' and resid 113 through 117 removed outlier: 5.891A pdb=" N TYR e 172 " --> pdb=" O ASN e 137 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 152 through 153 Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.727A pdb=" N MET F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.863A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.101A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 131 through 132 removed outlier: 6.101A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AG8, first strand: chain 'f' and resid 4 through 7 removed outlier: 3.921A pdb=" N GLU f 70 " --> pdb=" O SER f 67 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU f 11 " --> pdb=" O GLU f 104 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU f 33 " --> pdb=" O TYR f 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR f 49 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP f 35 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU f 11 " --> pdb=" O GLU f 104 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR f 96 " --> pdb=" O GLN f 90 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'f' and resid 113 through 117 removed outlier: 5.900A pdb=" N TYR f 172 " --> pdb=" O ASN f 137 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 152 through 153 Processing sheet with id=AH4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.693A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.806A pdb=" N VAL G 102 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.263A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 131 through 132 removed outlier: 3.538A pdb=" N THR G 135 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 151 through 154 removed outlier: 4.543A pdb=" N TYR G 194 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'g' and resid 4 through 7 removed outlier: 3.914A pdb=" N GLU g 70 " --> pdb=" O SER g 67 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 10 through 13 removed outlier: 6.492A pdb=" N LEU g 33 " --> pdb=" O TYR g 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR g 49 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP g 35 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'g' and resid 10 through 13 removed outlier: 3.516A pdb=" N THR g 96 " --> pdb=" O GLN g 90 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 113 through 117 removed outlier: 5.732A pdb=" N TYR g 172 " --> pdb=" O ASN g 137 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 152 through 153 Processing sheet with id=AI6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AI7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.706A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.817A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.290A pdb=" N ALA H 137 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL H 184 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 131 through 132 removed outlier: 5.290A pdb=" N ALA H 137 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL H 184 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AJ3, first strand: chain 'h' and resid 4 through 7 removed outlier: 3.955A pdb=" N GLU h 70 " --> pdb=" O SER h 67 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.495A pdb=" N LEU h 33 " --> pdb=" O TYR h 49 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR h 49 " --> pdb=" O LEU h 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP h 35 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'h' and resid 10 through 13 removed outlier: 3.584A pdb=" N THR h 96 " --> pdb=" O GLN h 90 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'h' and resid 113 through 117 removed outlier: 5.903A pdb=" N TYR h 172 " --> pdb=" O ASN h 137 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'h' and resid 144 through 149 Processing sheet with id=AJ8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AJ9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.690A pdb=" N MET I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.900A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 120 through 124 removed outlier: 6.134A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 131 through 132 removed outlier: 6.134A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AK5, first strand: chain 'i' and resid 4 through 7 removed outlier: 3.898A pdb=" N GLU i 70 " --> pdb=" O SER i 67 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.441A pdb=" N LEU i 33 " --> pdb=" O TYR i 49 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR i 49 " --> pdb=" O LEU i 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP i 35 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'i' and resid 10 through 13 removed outlier: 3.533A pdb=" N THR i 96 " --> pdb=" O GLN i 90 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'i' and resid 113 through 117 removed outlier: 5.904A pdb=" N TYR i 172 " --> pdb=" O ASN i 137 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'i' and resid 152 through 153 Processing sheet with id=AL1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AL2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.740A pdb=" N MET J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.747A pdb=" N VAL J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'J' and resid 120 through 124 removed outlier: 6.136A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 131 through 132 removed outlier: 6.136A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER J 177 " --> pdb=" O VAL J 169 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 151 through 154 Processing sheet with id=AL7, first strand: chain 'j' and resid 4 through 7 removed outlier: 3.800A pdb=" N GLU j 70 " --> pdb=" O SER j 67 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'j' and resid 10 through 13 removed outlier: 3.567A pdb=" N LEU j 11 " --> pdb=" O LYS j 102 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU j 33 " --> pdb=" O TYR j 49 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR j 49 " --> pdb=" O LEU j 33 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP j 35 " --> pdb=" O LEU j 47 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'j' and resid 10 through 13 removed outlier: 3.567A pdb=" N LEU j 11 " --> pdb=" O LYS j 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR j 96 " --> pdb=" O GLN j 90 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'j' and resid 113 through 117 removed outlier: 6.035A pdb=" N TYR j 172 " --> pdb=" O ASN j 137 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'j' and resid 152 through 153 Processing sheet with id=AM3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AM4, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.748A pdb=" N MET K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.739A pdb=" N VAL K 102 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.311A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'K' and resid 131 through 132 removed outlier: 3.519A pdb=" N THR K 135 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AM9, first strand: chain 'k' and resid 4 through 7 removed outlier: 3.877A pdb=" N GLU k 70 " --> pdb=" O SER k 67 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'k' and resid 10 through 13 removed outlier: 6.544A pdb=" N LEU k 33 " --> pdb=" O TYR k 49 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR k 49 " --> pdb=" O LEU k 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP k 35 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'k' and resid 10 through 13 removed outlier: 3.543A pdb=" N THR k 96 " --> pdb=" O GLN k 90 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'k' and resid 113 through 117 removed outlier: 6.003A pdb=" N TYR k 172 " --> pdb=" O ASN k 137 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'k' and resid 152 through 153 Processing sheet with id=AN5, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AN6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.749A pdb=" N MET L 34 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.796A pdb=" N VAL L 102 " --> pdb=" O LYS L 94 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'L' and resid 120 through 124 removed outlier: 5.277A pdb=" N ALA L 137 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL L 184 " --> pdb=" O ALA L 137 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY L 139 " --> pdb=" O VAL L 182 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL L 182 " --> pdb=" O GLY L 139 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU L 141 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER L 180 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS L 143 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU L 178 " --> pdb=" O LYS L 143 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'L' and resid 131 through 132 removed outlier: 3.566A pdb=" N THR L 135 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ALA L 137 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL L 184 " --> pdb=" O ALA L 137 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY L 139 " --> pdb=" O VAL L 182 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL L 182 " --> pdb=" O GLY L 139 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU L 141 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER L 180 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS L 143 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU L 178 " --> pdb=" O LYS L 143 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L' and resid 151 through 154 Processing sheet with id=AO2, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.901A pdb=" N GLU l 70 " --> pdb=" O SER l 67 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'l' and resid 10 through 13 removed outlier: 6.552A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.529A pdb=" N THR l 96 " --> pdb=" O GLN l 90 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 113 through 117 removed outlier: 5.895A pdb=" N TYR l 172 " --> pdb=" O ASN l 137 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'l' and resid 152 through 153 Processing sheet with id=AO7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AO8, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.729A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.821A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'M' and resid 120 through 124 removed outlier: 5.273A pdb=" N ALA M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL M 184 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY M 139 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL M 182 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU M 141 " --> pdb=" O SER M 180 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER M 180 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS M 143 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU M 178 " --> pdb=" O LYS M 143 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'M' and resid 131 through 132 removed outlier: 5.273A pdb=" N ALA M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL M 184 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY M 139 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL M 182 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU M 141 " --> pdb=" O SER M 180 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER M 180 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS M 143 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU M 178 " --> pdb=" O LYS M 143 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'M' and resid 151 through 154 Processing sheet with id=AP4, first strand: chain 'm' and resid 4 through 7 removed outlier: 3.909A pdb=" N GLU m 70 " --> pdb=" O SER m 67 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'm' and resid 10 through 13 removed outlier: 6.504A pdb=" N LEU m 11 " --> pdb=" O GLU m 104 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU m 33 " --> pdb=" O TYR m 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR m 49 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP m 35 " --> pdb=" O LEU m 47 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'm' and resid 10 through 13 removed outlier: 6.504A pdb=" N LEU m 11 " --> pdb=" O GLU m 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR m 96 " --> pdb=" O GLN m 90 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'm' and resid 113 through 117 removed outlier: 5.962A pdb=" N TYR m 172 " --> pdb=" O ASN m 137 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'm' and resid 152 through 153 Processing sheet with id=AP9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AQ1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.697A pdb=" N MET N 34 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.771A pdb=" N VAL N 102 " --> pdb=" O LYS N 94 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'N' and resid 120 through 124 removed outlier: 6.183A pdb=" N TYR N 176 " --> pdb=" O ASP N 144 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'N' and resid 131 through 132 removed outlier: 3.553A pdb=" N THR N 135 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR N 176 " --> pdb=" O ASP N 144 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'N' and resid 151 through 154 removed outlier: 4.720A pdb=" N TYR N 194 " --> pdb=" O VAL N 211 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'n' and resid 4 through 7 removed outlier: 3.831A pdb=" N GLU n 70 " --> pdb=" O SER n 67 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'n' and resid 10 through 13 removed outlier: 6.535A pdb=" N LEU n 33 " --> pdb=" O TYR n 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR n 49 " --> pdb=" O LEU n 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP n 35 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.622A pdb=" N THR n 96 " --> pdb=" O GLN n 90 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'n' and resid 113 through 117 removed outlier: 5.997A pdb=" N TYR n 172 " --> pdb=" O ASN n 137 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'n' and resid 152 through 153 2175 hydrogen bonds defined for protein. 5325 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: 20.55 Time building geometry restraints manager: 15.50 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: 15139 1.34 - 1.46: 12248 1.46 - 1.58: 20946 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 48529 Sorted by residual: bond pdb=" CB VAL D 100F" pdb=" CG1 VAL D 100F" ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.67e+00 bond pdb=" CB TRP D 36 " pdb=" CG TRP D 36 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.59e+00 bond pdb=" C GLN e 38 " pdb=" N LYS e 39 " ideal model delta sigma weight residual 1.340 1.231 0.109 5.87e-02 2.90e+02 3.46e+00 bond pdb=" CB TRP I 36 " pdb=" CG TRP I 36 " ideal model delta sigma weight residual 1.498 1.441 0.057 3.10e-02 1.04e+03 3.37e+00 bond pdb=" CB ILE D 50 " pdb=" CG2 ILE D 50 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.25e+00 ... (remaining 48524 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.25: 1301 106.25 - 113.22: 26830 113.22 - 120.19: 15559 120.19 - 127.16: 21808 127.16 - 134.13: 595 Bond angle restraints: 66093 Sorted by residual: angle pdb=" C ASN X 19 " pdb=" N PRO X 20 " pdb=" CA PRO X 20 " ideal model delta sigma weight residual 127.00 133.47 -6.47 2.40e+00 1.74e-01 7.26e+00 angle pdb=" C SER n 7 " pdb=" N PRO n 8 " pdb=" CD PRO n 8 " ideal model delta sigma weight residual 120.60 125.98 -5.38 2.20e+00 2.07e-01 5.99e+00 angle pdb=" C SER k 7 " pdb=" N PRO k 8 " pdb=" CD PRO k 8 " ideal model delta sigma weight residual 120.60 125.74 -5.14 2.20e+00 2.07e-01 5.46e+00 angle pdb=" C LYS c 50 " pdb=" N ALA c 51 " pdb=" CA ALA c 51 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.94e+00 angle pdb=" CA CYS i 193 " pdb=" CB CYS i 193 " pdb=" SG CYS i 193 " ideal model delta sigma weight residual 114.40 119.50 -5.10 2.30e+00 1.89e-01 4.92e+00 ... (remaining 66088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 27296 15.41 - 30.83: 1071 30.83 - 46.24: 355 46.24 - 61.65: 110 61.65 - 77.07: 30 Dihedral angle restraints: 28862 sinusoidal: 10890 harmonic: 17972 Sorted by residual: dihedral pdb=" CA HIS M 35 " pdb=" C HIS M 35 " pdb=" N TRP M 36 " pdb=" CA TRP M 36 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA HIS J 35 " pdb=" C HIS J 35 " pdb=" N TRP J 36 " pdb=" CA TRP J 36 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA HIS D 35 " pdb=" C HIS D 35 " pdb=" N TRP D 36 " pdb=" CA TRP D 36 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 28859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 5038 0.041 - 0.082: 1624 0.082 - 0.123: 680 0.123 - 0.163: 59 0.163 - 0.204: 4 Chirality restraints: 7405 Sorted by residual: chirality pdb=" CB ILE D 69 " pdb=" CA ILE D 69 " pdb=" CG1 ILE D 69 " pdb=" CG2 ILE D 69 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE K 69 " pdb=" CA ILE K 69 " pdb=" CG1 ILE K 69 " pdb=" CG2 ILE K 69 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CB ILE I 69 " pdb=" CA ILE I 69 " pdb=" CG1 ILE I 69 " pdb=" CG2 ILE I 69 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 7402 not shown) Planarity restraints: 8452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 47 " 0.005 2.00e-02 2.50e+03 1.39e-02 4.82e+00 pdb=" CG TRP D 47 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 47 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 47 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 47 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 47 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 47 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 148 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO C 149 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 148 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 149 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.025 5.00e-02 4.00e+02 ... (remaining 8449 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3116 2.73 - 3.27: 43876 3.27 - 3.82: 78732 3.82 - 4.36: 96049 4.36 - 4.90: 167644 Nonbonded interactions: 389417 Sorted by model distance: nonbonded pdb=" O TYR a 185 " pdb=" OH TYR a 191 " model vdw 2.188 2.440 nonbonded pdb=" O TYR b 185 " pdb=" OH TYR b 191 " model vdw 2.205 2.440 nonbonded pdb=" O VAL N 100F" pdb=" OH TYR n 36 " model vdw 2.206 2.440 nonbonded pdb=" O TYR d 185 " pdb=" OH TYR d 191 " model vdw 2.222 2.440 nonbonded pdb=" OG SER c 12 " pdb=" OE1 GLU c 104 " model vdw 2.232 2.440 ... (remaining 389412 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' } 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' } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.430 Construct map_model_manager: 0.030 Extract box with map and model: 9.540 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 102.290 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.370 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 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 : 0.008 0.109 48529 Z= 0.519 Angle : 0.606 6.465 66093 Z= 0.324 Chirality : 0.046 0.204 7405 Planarity : 0.005 0.049 8452 Dihedral : 10.498 77.066 17188 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.17 (0.10), residues: 6157 helix: -2.01 (0.24), residues: 210 sheet: 0.35 (0.09), residues: 2996 loop : 0.18 (0.12), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 47 HIS 0.010 0.002 HIS G 35 PHE 0.025 0.002 PHE l 62 TYR 0.033 0.003 TYR H 91 ARG 0.013 0.001 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1481 time to evaluate : 4.152 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: A 59 TYR cc_start: 0.6870 (m-80) cc_final: 0.6663 (m-10) REVERT: A 101 ASP cc_start: 0.7001 (p0) cc_final: 0.6584 (p0) REVERT: D 34 MET cc_start: 0.7651 (mmm) cc_final: 0.7337 (mmp) REVERT: d 31 ASN cc_start: 0.8025 (p0) cc_final: 0.7552 (p0) REVERT: e 169 ASP cc_start: 0.7603 (p0) cc_final: 0.7239 (p0) REVERT: h 65 SER cc_start: 0.8573 (t) cc_final: 0.8328 (p) REVERT: X 37 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8080 (p0) REVERT: I 100 ASP cc_start: 0.7946 (m-30) cc_final: 0.7286 (m-30) REVERT: i 2 ILE cc_start: 0.8373 (mt) cc_final: 0.8152 (mt) REVERT: J 53 ASP cc_start: 0.7446 (p0) cc_final: 0.7209 (p0) REVERT: K 34 MET cc_start: 0.7799 (mmm) cc_final: 0.7508 (mmt) REVERT: L 72 ASP cc_start: 0.8331 (t0) cc_final: 0.7957 (t0) REVERT: l 172 TYR cc_start: 0.7576 (m-80) cc_final: 0.7092 (m-80) REVERT: M 75 LYS cc_start: 0.9167 (mttt) cc_final: 0.8918 (mttm) REVERT: n 2 ILE cc_start: 0.7736 (mt) cc_final: 0.7536 (mt) outliers start: 4 outliers final: 1 residues processed: 1485 average time/residue: 0.5667 time to fit residues: 1322.7998 Evaluate side-chains 759 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 757 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 37 ASN Chi-restraints excluded: chain X residue 85 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 517 optimal weight: 5.9990 chunk 464 optimal weight: 8.9990 chunk 257 optimal weight: 0.0970 chunk 158 optimal weight: 0.7980 chunk 313 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 480 optimal weight: 30.0000 chunk 185 optimal weight: 0.4980 chunk 292 optimal weight: 3.9990 chunk 357 optimal weight: 0.8980 chunk 556 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 100CASN B 171 GLN B 199 ASN C 100CASN c 136 ASN D 199 ASN d 37 GLN d 123 GLN E 56 ASN E 171 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 199 ASN G 171 GLN g 27 GLN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN h 136 ASN h 198 GLN I 100CASN I 171 GLN i 146 GLN j 37 GLN K 105 GLN l 123 GLN M 199 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 GLN N 3 GLN N 100CASN n 137 ASN n 151 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 48529 Z= 0.163 Angle : 0.571 9.103 66093 Z= 0.300 Chirality : 0.043 0.179 7405 Planarity : 0.005 0.065 8452 Dihedral : 4.441 24.075 6638 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.65 % Allowed : 10.23 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.79 (0.11), residues: 6157 helix: -0.20 (0.32), residues: 210 sheet: 0.79 (0.09), residues: 3080 loop : 0.43 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 96 HIS 0.010 0.001 HIS n 197 PHE 0.026 0.002 PHE A 29 TYR 0.028 0.002 TYR B 52A ARG 0.008 0.001 ARG f 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 924 time to evaluate : 4.175 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: A 101 ASP cc_start: 0.6793 (p0) cc_final: 0.6411 (p0) REVERT: B 105 GLN cc_start: 0.5495 (tp40) cc_final: 0.5292 (tp40) REVERT: b 116 ILE cc_start: 0.6716 (mm) cc_final: 0.6374 (mt) REVERT: D 19 ARG cc_start: 0.7971 (ttt90) cc_final: 0.7724 (ttm-80) REVERT: E 100 ASP cc_start: 0.8080 (m-30) cc_final: 0.7788 (m-30) REVERT: e 151 ASN cc_start: 0.6399 (t0) cc_final: 0.6194 (t0) REVERT: f 209 ASN cc_start: 0.6712 (m-40) cc_final: 0.6480 (m-40) REVERT: G 171 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: h 10 THR cc_start: 0.8600 (m) cc_final: 0.8331 (p) REVERT: h 194 GLU cc_start: 0.5554 (tp30) cc_final: 0.5241 (tp30) REVERT: I 72 ASP cc_start: 0.7868 (t0) cc_final: 0.7632 (t0) REVERT: I 100 ASP cc_start: 0.7748 (m-30) cc_final: 0.7081 (m-30) REVERT: J 53 ASP cc_start: 0.7588 (p0) cc_final: 0.7320 (p0) REVERT: J 99 GLU cc_start: 0.5922 (mt-10) cc_final: 0.4959 (mt-10) REVERT: k 139 TYR cc_start: 0.5787 (t80) cc_final: 0.5496 (t80) REVERT: L 3 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7482 (tp40) REVERT: L 170 LEU cc_start: 0.8428 (tp) cc_final: 0.8033 (tt) REVERT: M 75 LYS cc_start: 0.9046 (mttt) cc_final: 0.8805 (mttm) REVERT: m 139 TYR cc_start: 0.5784 (t80) cc_final: 0.5511 (t80) outliers start: 88 outliers final: 51 residues processed: 988 average time/residue: 0.5181 time to fit residues: 835.1566 Evaluate side-chains 785 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 733 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 28 SER Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 CYS Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain e residue 1 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 142 GLU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain h residue 31 ASN Chi-restraints excluded: chain h residue 145 VAL Chi-restraints excluded: chain h residue 198 GLN Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 199 ASN Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 309 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 463 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 557 optimal weight: 4.9990 chunk 602 optimal weight: 7.9990 chunk 496 optimal weight: 0.0970 chunk 553 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 447 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 100CASN D 199 ASN d 27 GLN d 37 GLN ** E 100CASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** e 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN F 100CASN G 171 GLN G 199 ASN g 37 GLN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 198 GLN I 56 ASN I 171 GLN i 37 GLN ** i 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AASN j 89 GLN ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 GLN L 171 GLN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 171 GLN n 79 GLN n 136 ASN n 146 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48529 Z= 0.278 Angle : 0.571 8.507 66093 Z= 0.302 Chirality : 0.043 0.181 7405 Planarity : 0.005 0.087 8452 Dihedral : 4.446 20.687 6634 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.36 % Allowed : 11.28 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.92 (0.11), residues: 6157 helix: 0.19 (0.33), residues: 210 sheet: 0.94 (0.09), residues: 3052 loop : 0.42 (0.12), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 96 HIS 0.006 0.001 HIS C 35 PHE 0.022 0.002 PHE c 115 TYR 0.025 0.002 TYR C 52A ARG 0.010 0.001 ARG m 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 765 time to evaluate : 4.196 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: A 29 PHE cc_start: 0.6287 (t80) cc_final: 0.6035 (t80) REVERT: A 52 TRP cc_start: 0.6709 (m-90) cc_final: 0.6486 (m-90) REVERT: A 101 ASP cc_start: 0.6740 (p0) cc_final: 0.6364 (p0) REVERT: D 19 ARG cc_start: 0.8129 (ttt90) cc_final: 0.7887 (ttm-80) REVERT: E 100 ASP cc_start: 0.8210 (m-30) cc_final: 0.7875 (m-30) REVERT: I 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7722 (t0) REVERT: J 53 ASP cc_start: 0.7690 (p0) cc_final: 0.7413 (p0) REVERT: L 170 LEU cc_start: 0.8347 (tp) cc_final: 0.8092 (tt) REVERT: M 75 LYS cc_start: 0.9119 (mttt) cc_final: 0.8894 (mttm) REVERT: m 139 TYR cc_start: 0.5832 (t80) cc_final: 0.5538 (t80) outliers start: 126 outliers final: 85 residues processed: 856 average time/residue: 0.4793 time to fit residues: 672.6198 Evaluate side-chains 771 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 686 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 28 SER Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 202 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 CYS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain e residue 1 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 166 ASP Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 199 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 550 optimal weight: 8.9990 chunk 419 optimal weight: 30.0000 chunk 289 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 374 optimal weight: 3.9990 chunk 559 optimal weight: 1.9990 chunk 592 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 530 optimal weight: 0.6980 chunk 159 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN c 37 GLN c 136 ASN E 3 GLN E 100CASN H 31 ASN I 171 GLN i 157 ASN J 82AASN ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN k 123 GLN L 56 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 159 GLN N 3 GLN N 171 GLN ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 48529 Z= 0.208 Angle : 0.546 8.766 66093 Z= 0.287 Chirality : 0.042 0.186 7405 Planarity : 0.004 0.085 8452 Dihedral : 4.377 19.443 6634 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.15 % Allowed : 12.34 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.94 (0.11), residues: 6157 helix: 0.42 (0.34), residues: 210 sheet: 0.90 (0.09), residues: 3094 loop : 0.47 (0.12), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 96 HIS 0.005 0.001 HIS C 35 PHE 0.020 0.002 PHE B 27 TYR 0.025 0.002 TYR C 52A ARG 0.008 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 732 time to evaluate : 4.186 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: A 59 TYR cc_start: 0.6622 (m-80) cc_final: 0.6395 (m-80) REVERT: A 101 ASP cc_start: 0.6641 (p0) cc_final: 0.6376 (p0) REVERT: c 193 CYS cc_start: 0.2373 (OUTLIER) cc_final: 0.1993 (t) REVERT: f 209 ASN cc_start: 0.6924 (m-40) cc_final: 0.6714 (m-40) REVERT: I 72 ASP cc_start: 0.8059 (t0) cc_final: 0.7692 (t0) REVERT: J 53 ASP cc_start: 0.7785 (p0) cc_final: 0.7502 (p0) REVERT: m 139 TYR cc_start: 0.5994 (t80) cc_final: 0.5661 (t80) outliers start: 115 outliers final: 86 residues processed: 817 average time/residue: 0.4778 time to fit residues: 646.6267 Evaluate side-chains 766 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 679 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain d residue 202 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 CYS Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain e residue 1 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain L residue 199 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 493 optimal weight: 0.8980 chunk 336 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 441 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 505 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 302 optimal weight: 7.9990 chunk 531 optimal weight: 2.9990 chunk 149 optimal weight: 0.0870 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 39 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 38 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 164 HIS C 199 ASN c 37 GLN c 136 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 GLN G 100CASN G 192 GLN H 31 ASN X 11 ASN ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 41 ASN I 56 ASN I 100CASN i 157 ASN J 82AASN j 31 ASN K 31 ASN K 76 ASN L 56 ASN L 199 ASN l 37 GLN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN n 165 GLN ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 48529 Z= 0.359 Angle : 0.592 10.254 66093 Z= 0.312 Chirality : 0.043 0.187 7405 Planarity : 0.005 0.086 8452 Dihedral : 4.572 21.901 6634 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.66 % Allowed : 12.74 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.70 (0.11), residues: 6157 helix: 0.12 (0.33), residues: 224 sheet: 0.75 (0.09), residues: 3122 loop : 0.30 (0.12), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 96 HIS 0.008 0.001 HIS C 35 PHE 0.022 0.002 PHE D 29 TYR 0.027 0.002 TYR C 52A ARG 0.010 0.001 ARG c 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 686 time to evaluate : 4.148 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: A 59 TYR cc_start: 0.6672 (m-80) cc_final: 0.6361 (m-80) REVERT: A 101 ASP cc_start: 0.6980 (p0) cc_final: 0.6647 (p0) REVERT: B 13 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7074 (mm-40) REVERT: c 193 CYS cc_start: 0.2549 (OUTLIER) cc_final: 0.2071 (t) REVERT: D 31 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7666 (t0) REVERT: H 124 LEU cc_start: 0.5204 (tp) cc_final: 0.4941 (tt) REVERT: h 142 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6280 (tm-30) REVERT: X 23 ASN cc_start: 0.8191 (t0) cc_final: 0.7986 (t0) REVERT: I 72 ASP cc_start: 0.8189 (t0) cc_final: 0.7151 (t0) REVERT: K 31 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7783 (t0) REVERT: K 72 ASP cc_start: 0.8409 (t0) cc_final: 0.8074 (t0) REVERT: K 82 MET cc_start: 0.6394 (mtm) cc_final: 0.6161 (mtp) REVERT: l 4 MET cc_start: 0.8228 (mmt) cc_final: 0.7992 (mmt) REVERT: l 70 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7695 (mm-30) REVERT: m 139 TYR cc_start: 0.6060 (t80) cc_final: 0.5500 (t80) outliers start: 142 outliers final: 101 residues processed: 793 average time/residue: 0.4669 time to fit residues: 613.8683 Evaluate side-chains 742 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 638 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain e residue 1 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 202 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain h residue 130 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain L residue 199 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 208 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 199 optimal weight: 0.0270 chunk 533 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 347 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 593 optimal weight: 4.9990 chunk 492 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN c 37 GLN E 3 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN X 11 ASN I 56 ASN I 100CASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 82AASN j 31 ASN K 76 ASN L 56 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 171 GLN ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 48529 Z= 0.191 Angle : 0.551 10.577 66093 Z= 0.287 Chirality : 0.042 0.209 7405 Planarity : 0.004 0.087 8452 Dihedral : 4.374 19.139 6634 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 13.78 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.77 (0.11), residues: 6157 helix: 0.18 (0.34), residues: 224 sheet: 0.82 (0.09), residues: 3094 loop : 0.33 (0.12), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 103 HIS 0.004 0.001 HIS L 200 PHE 0.031 0.002 PHE A 146 TYR 0.030 0.002 TYR b 139 ARG 0.011 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 693 time to evaluate : 5.262 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: A 101 ASP cc_start: 0.6523 (p0) cc_final: 0.6264 (p0) REVERT: c 193 CYS cc_start: 0.2400 (OUTLIER) cc_final: 0.2032 (t) REVERT: F 79 TYR cc_start: 0.8774 (m-10) cc_final: 0.8459 (m-10) REVERT: h 142 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6263 (tm-30) REVERT: I 72 ASP cc_start: 0.7911 (t0) cc_final: 0.7537 (t0) REVERT: L 79 TYR cc_start: 0.8766 (m-80) cc_final: 0.8347 (m-10) REVERT: L 197 ASN cc_start: 0.5504 (OUTLIER) cc_final: 0.5036 (m-40) outliers start: 108 outliers final: 86 residues processed: 770 average time/residue: 0.4795 time to fit residues: 612.2850 Evaluate side-chains 738 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 650 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 202 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain h residue 130 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 171 GLN Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 184 ASP Chi-restraints excluded: chain n residue 208 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 571 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 337 optimal weight: 0.8980 chunk 433 optimal weight: 50.0000 chunk 335 optimal weight: 4.9990 chunk 499 optimal weight: 0.9980 chunk 331 optimal weight: 3.9990 chunk 590 optimal weight: 20.0000 chunk 369 optimal weight: 9.9990 chunk 360 optimal weight: 0.6980 chunk 272 optimal weight: 20.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN X 11 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AASN K 31 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 GLN ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48529 Z= 0.201 Angle : 0.555 11.269 66093 Z= 0.288 Chirality : 0.042 0.262 7405 Planarity : 0.004 0.087 8452 Dihedral : 4.308 18.702 6634 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.98 % Allowed : 14.36 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.80 (0.11), residues: 6157 helix: 0.35 (0.34), residues: 224 sheet: 0.83 (0.09), residues: 3108 loop : 0.34 (0.12), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 103 HIS 0.004 0.001 HIS C 35 PHE 0.044 0.002 PHE A 146 TYR 0.025 0.002 TYR B 52A ARG 0.012 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 689 time to evaluate : 4.158 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: A 101 ASP cc_start: 0.6305 (p0) cc_final: 0.5968 (p0) REVERT: c 193 CYS cc_start: 0.2351 (OUTLIER) cc_final: 0.1981 (t) REVERT: F 79 TYR cc_start: 0.8772 (m-10) cc_final: 0.8464 (m-10) REVERT: F 83 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7895 (mtm-85) REVERT: G 72 ASP cc_start: 0.8366 (t0) cc_final: 0.8149 (t0) REVERT: h 142 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6159 (tm-30) REVERT: J 166 PHE cc_start: 0.2439 (m-80) cc_final: 0.2154 (m-10) REVERT: K 31 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7632 (t0) REVERT: K 72 ASP cc_start: 0.8366 (t70) cc_final: 0.8066 (t0) REVERT: L 197 ASN cc_start: 0.5495 (OUTLIER) cc_final: 0.5075 (m-40) REVERT: l 70 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7527 (mm-30) REVERT: n 147 TRP cc_start: 0.4759 (m100) cc_final: 0.4518 (m100) outliers start: 106 outliers final: 90 residues processed: 764 average time/residue: 0.4664 time to fit residues: 588.7842 Evaluate side-chains 747 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 654 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain e residue 1 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 202 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 184 ASP Chi-restraints excluded: chain n residue 208 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 365 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 352 optimal weight: 0.0020 chunk 177 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 375 optimal weight: 2.9990 chunk 402 optimal weight: 10.0000 chunk 292 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 76 ASN A 100CASN B 56 ASN C 31 ASN ** c 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 GLN E 3 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN X 11 ASN ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN I 100CASN j 90 GLN K 31 ASN L 56 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 48529 Z= 0.345 Angle : 0.611 12.055 66093 Z= 0.319 Chirality : 0.044 0.391 7405 Planarity : 0.005 0.090 8452 Dihedral : 4.568 21.804 6634 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.24 % Allowed : 14.55 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.60 (0.11), residues: 6157 helix: 0.40 (0.34), residues: 224 sheet: 0.69 (0.09), residues: 3122 loop : 0.20 (0.12), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 103 HIS 0.007 0.001 HIS C 35 PHE 0.031 0.002 PHE c 71 TYR 0.044 0.002 TYR A 176 ARG 0.013 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 664 time to evaluate : 4.139 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: C 34 MET cc_start: 0.7884 (mmm) cc_final: 0.7411 (mmm) REVERT: c 193 CYS cc_start: 0.2306 (OUTLIER) cc_final: 0.1952 (t) REVERT: D 31 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7729 (t0) REVERT: G 72 ASP cc_start: 0.8528 (t0) cc_final: 0.8294 (t0) REVERT: h 142 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6296 (tm-30) REVERT: I 82 MET cc_start: 0.7202 (mtm) cc_final: 0.7000 (mtm) REVERT: J 119 PRO cc_start: 0.1788 (Cg_exo) cc_final: 0.1471 (Cg_endo) REVERT: K 72 ASP cc_start: 0.8479 (t70) cc_final: 0.8134 (t0) REVERT: k 55 GLU cc_start: 0.7690 (tp30) cc_final: 0.7454 (tm-30) REVERT: L 208 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6962 (t0) REVERT: l 104 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.5069 (mt-10) REVERT: M 85 GLU cc_start: 0.8519 (pm20) cc_final: 0.8198 (pm20) REVERT: M 86 ASP cc_start: 0.8028 (m-30) cc_final: 0.7706 (t0) outliers start: 120 outliers final: 99 residues processed: 746 average time/residue: 0.4617 time to fit residues: 571.4305 Evaluate side-chains 724 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 621 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain a residue 108 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain d residue 166 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 202 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain X residue 13 ASN Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain L residue 208 ASP Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 104 GLU Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 168 LYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 184 ASP Chi-restraints excluded: chain n residue 208 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 537 optimal weight: 0.5980 chunk 566 optimal weight: 6.9990 chunk 516 optimal weight: 6.9990 chunk 550 optimal weight: 6.9990 chunk 565 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 432 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 497 optimal weight: 0.9990 chunk 520 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 100CASN a 38 GLN B 56 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 48529 Z= 0.336 Angle : 0.616 13.256 66093 Z= 0.321 Chirality : 0.044 0.279 7405 Planarity : 0.005 0.091 8452 Dihedral : 4.613 23.247 6634 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.17 % Allowed : 15.32 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.49 (0.11), residues: 6157 helix: 0.38 (0.34), residues: 224 sheet: 0.60 (0.09), residues: 3122 loop : 0.14 (0.12), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP e 147 HIS 0.006 0.001 HIS C 35 PHE 0.031 0.002 PHE C 146 TYR 0.040 0.002 TYR A 176 ARG 0.014 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 655 time to evaluate : 4.533 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: A 105 GLN cc_start: 0.7336 (pp30) cc_final: 0.7124 (pp30) REVERT: C 34 MET cc_start: 0.7867 (mmm) cc_final: 0.7383 (mmm) REVERT: c 193 CYS cc_start: 0.2298 (OUTLIER) cc_final: 0.1926 (t) REVERT: D 212 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6672 (mp0) REVERT: e 55 GLU cc_start: 0.8411 (tp30) cc_final: 0.7940 (tm-30) REVERT: G 72 ASP cc_start: 0.8523 (t0) cc_final: 0.8292 (t0) REVERT: h 142 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6308 (tm-30) REVERT: K 72 ASP cc_start: 0.8486 (t70) cc_final: 0.8203 (t0) REVERT: L 208 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7009 (t0) REVERT: l 104 GLU cc_start: 0.5347 (OUTLIER) cc_final: 0.5053 (mt-10) REVERT: M 85 GLU cc_start: 0.8536 (pm20) cc_final: 0.8224 (pm20) REVERT: M 86 ASP cc_start: 0.8019 (m-30) cc_final: 0.7716 (t0) REVERT: m 139 TYR cc_start: 0.6428 (t80) cc_final: 0.5970 (t80) REVERT: n 147 TRP cc_start: 0.4789 (m100) cc_final: 0.4435 (m100) outliers start: 116 outliers final: 100 residues processed: 739 average time/residue: 0.4713 time to fit residues: 579.6322 Evaluate side-chains 735 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 632 time to evaluate : 4.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain e residue 132 VAL Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 202 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 108 THR Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 17 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain L residue 208 ASP Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 104 GLU Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain m residue 131 VAL Chi-restraints excluded: chain m residue 168 LYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 184 ASP Chi-restraints excluded: chain n residue 208 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 548 optimal weight: 0.9980 chunk 361 optimal weight: 0.8980 chunk 582 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 404 optimal weight: 0.9990 chunk 610 optimal weight: 20.0000 chunk 562 optimal weight: 5.9990 chunk 486 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 375 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN b 146 GLN C 76 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN H 31 ASN h 79 GLN I 76 ASN I 100CASN L 56 ASN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48529 Z= 0.178 Angle : 0.589 13.663 66093 Z= 0.304 Chirality : 0.043 0.221 7405 Planarity : 0.004 0.091 8452 Dihedral : 4.380 22.792 6634 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.57 % Allowed : 16.25 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.65 (0.11), residues: 6157 helix: 0.53 (0.35), residues: 224 sheet: 0.71 (0.09), residues: 3122 loop : 0.24 (0.13), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP j 95 HIS 0.004 0.001 HIS J 35 PHE 0.025 0.001 PHE A 146 TYR 0.041 0.002 TYR A 100D ARG 0.014 0.001 ARG k 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12314 Ramachandran restraints generated. 6157 Oldfield, 0 Emsley, 6157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 697 time to evaluate : 4.226 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: A 145 TYR cc_start: 0.5383 (p90) cc_final: 0.5139 (p90) REVERT: c 193 CYS cc_start: 0.2307 (OUTLIER) cc_final: 0.1983 (t) REVERT: D 31 ASN cc_start: 0.7970 (t0) cc_final: 0.7619 (t0) REVERT: D 212 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6660 (mp0) REVERT: e 55 GLU cc_start: 0.8402 (tp30) cc_final: 0.7965 (tm-30) REVERT: F 79 TYR cc_start: 0.8757 (m-10) cc_final: 0.8499 (m-10) REVERT: G 72 ASP cc_start: 0.8366 (t0) cc_final: 0.8162 (t0) REVERT: H 72 ASP cc_start: 0.7974 (t0) cc_final: 0.7426 (t0) REVERT: h 142 GLU cc_start: 0.6646 (tm-30) cc_final: 0.6221 (tm-30) REVERT: J 119 PRO cc_start: 0.1478 (Cg_exo) cc_final: 0.1119 (Cg_endo) REVERT: K 72 ASP cc_start: 0.8400 (t70) cc_final: 0.8132 (t0) REVERT: L 79 TYR cc_start: 0.8629 (m-10) cc_final: 0.8378 (m-10) REVERT: M 85 GLU cc_start: 0.8528 (pm20) cc_final: 0.8214 (pm20) REVERT: M 86 ASP cc_start: 0.7936 (m-30) cc_final: 0.7722 (t0) REVERT: m 139 TYR cc_start: 0.6330 (t80) cc_final: 0.5957 (t80) outliers start: 84 outliers final: 75 residues processed: 755 average time/residue: 0.4803 time to fit residues: 599.3837 Evaluate side-chains 729 residues out of total 5375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 653 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 193 CYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 132 VAL Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 160 GLU Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 202 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 176 TYR Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain i residue 21 ILE Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain i residue 196 THR Chi-restraints excluded: chain i residue 208 PHE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 95 TRP Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 197 ASN Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 166 ASP Chi-restraints excluded: chain l residue 180 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 117 LYS Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 298 optimal weight: 20.0000 chunk 386 optimal weight: 0.9990 chunk 518 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 448 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 487 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 500 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN ** c 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 ASN L 56 ASN l 159 GLN ** m 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.146558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090894 restraints weight = 95339.328| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.99 r_work: 0.3140 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 48529 Z= 0.293 Angle : 0.615 13.296 66093 Z= 0.319 Chirality : 0.044 0.204 7405 Planarity : 0.005 0.092 8452 Dihedral : 4.489 22.653 6634 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.65 % Allowed : 16.46 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.38 % 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: 0.55 (0.11), residues: 6157 helix: 0.62 (0.35), residues: 224 sheet: 0.65 (0.09), residues: 3122 loop : 0.16 (0.13), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP j 95 HIS 0.006 0.001 HIS H 35 PHE 0.031 0.002 PHE f 115 TYR 0.035 0.002 TYR A 176 ARG 0.015 0.001 ARG k 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12693.68 seconds wall clock time: 228 minutes 35.17 seconds (13715.17 seconds total)