Starting phenix.real_space_refine on Mon Mar 25 02:28:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x25_32958/03_2024/7x25_32958_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x25_32958/03_2024/7x25_32958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x25_32958/03_2024/7x25_32958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x25_32958/03_2024/7x25_32958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x25_32958/03_2024/7x25_32958_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x25_32958/03_2024/7x25_32958_neut.pdb" } resolution = 2.49 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= 0.000 sd= 0.002 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 8700 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 183 5.16 5 C 23480 2.51 5 N 6191 2.21 5 O 7256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G GLU 376": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G ARG 505": "NH1" <-> "NH2" Residue "G GLU 589": "OE1" <-> "OE2" Residue "G ARG 700": "NH1" <-> "NH2" Residue "G GLU 793": "OE1" <-> "OE2" Residue "G GLU 818": "OE1" <-> "OE2" Residue "G GLU 875": "OE1" <-> "OE2" Residue "G GLU 891": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G GLU 1017": "OE1" <-> "OE2" Residue "G GLU 1039": "OE1" <-> "OE2" Residue "G GLU 1062": "OE1" <-> "OE2" Residue "G ARG 1179": "NH1" <-> "NH2" Residue "G GLU 1183": "OE1" <-> "OE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "I GLU 32": "OE1" <-> "OE2" Residue "I TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 247": "OE1" <-> "OE2" Residue "I TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I ARG 505": "NH1" <-> "NH2" Residue "I PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 666": "OE1" <-> "OE2" Residue "I GLU 680": "OE1" <-> "OE2" Residue "I ARG 700": "NH1" <-> "NH2" Residue "I GLU 725": "OE1" <-> "OE2" Residue "I GLU 793": "OE1" <-> "OE2" Residue "I GLU 818": "OE1" <-> "OE2" Residue "I GLU 875": "OE1" <-> "OE2" Residue "I GLU 891": "OE1" <-> "OE2" Residue "I GLU 1039": "OE1" <-> "OE2" Residue "I GLU 1062": "OE1" <-> "OE2" Residue "I ARG 1179": "NH1" <-> "NH2" Residue "I GLU 1183": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "J GLU 376": "OE1" <-> "OE2" Residue "J GLU 379": "OE1" <-> "OE2" Residue "J GLU 382": "OE1" <-> "OE2" Residue "J ARG 505": "NH1" <-> "NH2" Residue "J GLU 589": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J GLU 680": "OE1" <-> "OE2" Residue "J ARG 700": "NH1" <-> "NH2" Residue "J GLU 725": "OE1" <-> "OE2" Residue "J GLU 793": "OE1" <-> "OE2" Residue "J GLU 818": "OE1" <-> "OE2" Residue "J GLU 875": "OE1" <-> "OE2" Residue "J GLU 891": "OE1" <-> "OE2" Residue "J GLU 1039": "OE1" <-> "OE2" Residue "J GLU 1090": "OE1" <-> "OE2" Residue "J GLU 1105": "OE1" <-> "OE2" Residue "J ARG 1179": "NH1" <-> "NH2" Residue "J GLU 1183": "OE1" <-> "OE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37110 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "C" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1573 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 213, 1573 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1599 Chain: "F" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9189 Classifications: {'peptide': 1189} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 215, 1582 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 215, 1582 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1611 Chain: "I" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9189 Classifications: {'peptide': 1189} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 9132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9132 Classifications: {'peptide': 1181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 58, 'TRANS': 1120} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 20.22, per 1000 atoms: 0.54 Number of scatterers: 37110 At special positions: 0 Unit cell: (153.715, 199.18, 240.315, 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 183 16.00 O 7256 8.00 N 6191 7.00 C 23480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 176 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 339 " - pdb=" SG CYS G 349 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 407 " distance=2.01 Simple disulfide: pdb=" SG CYS G 425 " - pdb=" SG CYS G 478 " distance=2.03 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 585 " distance=2.02 Simple disulfide: pdb=" SG CYS G 503 " - pdb=" SG CYS G 526 " distance=2.03 Simple disulfide: pdb=" SG CYS G 603 " - pdb=" SG CYS G 654 " distance=2.03 Simple disulfide: pdb=" SG CYS G 620 " - pdb=" SG CYS G 650 " distance=2.03 Simple disulfide: pdb=" SG CYS G 727 " - pdb=" SG CYS G 736 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.03 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 185 " - pdb=" SG CYS I 237 " distance=2.03 Simple disulfide: pdb=" SG CYS I 339 " - pdb=" SG CYS I 349 " distance=2.03 Simple disulfide: pdb=" SG CYS I 383 " - pdb=" SG CYS I 407 " distance=2.02 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 585 " distance=2.08 Simple disulfide: pdb=" SG CYS I 503 " - pdb=" SG CYS I 526 " distance=2.02 Simple disulfide: pdb=" SG CYS I 603 " - pdb=" SG CYS I 654 " distance=2.03 Simple disulfide: pdb=" SG CYS I 620 " - pdb=" SG CYS I 650 " distance=2.04 Simple disulfide: pdb=" SG CYS I 727 " - pdb=" SG CYS I 736 " distance=2.02 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.03 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=2.03 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1106 " - pdb=" SG CYS I1117 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.03 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.03 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.01 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.03 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.03 Simple disulfide: pdb=" SG CYS J 806 " - pdb=" SG CYS J 828 " distance=2.03 Simple disulfide: pdb=" SG CYS J 811 " - pdb=" SG CYS J 817 " distance=2.03 Simple disulfide: pdb=" SG CYS J 912 " - pdb=" SG CYS J 925 " distance=2.03 Simple disulfide: pdb=" SG CYS J1106 " - pdb=" SG CYS J1117 " distance=2.03 Simple disulfide: pdb=" SG CYS J1156 " - pdb=" SG CYS J1164 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 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: 11.91 Conformation dependent library (CDL) restraints added in 7.4 seconds 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8978 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 86 sheets defined 18.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.652A pdb=" N SER C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 removed outlier: 4.096A pdb=" N PHE G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 222 through 232 removed outlier: 4.006A pdb=" N TYR G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER G 390 " --> pdb=" O PRO G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 399 Processing helix chain 'G' and resid 411 through 416 Processing helix chain 'G' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER G 435 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 453 removed outlier: 3.636A pdb=" N MET G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 528 removed outlier: 4.047A pdb=" N SER G 528 " --> pdb=" O PRO G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 595 Processing helix chain 'G' and resid 805 through 812 Processing helix chain 'G' and resid 814 through 823 removed outlier: 3.616A pdb=" N GLN G 819 " --> pdb=" O GLN G 815 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU G 820 " --> pdb=" O LYS G 816 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 823 " --> pdb=" O GLN G 819 " (cutoff:3.500A) Processing helix chain 'G' and resid 826 through 854 removed outlier: 3.600A pdb=" N LYS G 830 " --> pdb=" O GLN G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 915 removed outlier: 3.711A pdb=" N CYS G 912 " --> pdb=" O GLY G 908 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET G 913 " --> pdb=" O TYR G 909 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN G 914 " --> pdb=" O ASP G 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 926 through 931 Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1012 removed outlier: 4.472A pdb=" N PHE G1012 " --> pdb=" O GLN G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1016 through 1039 removed outlier: 3.601A pdb=" N LEU G1036 " --> pdb=" O ALA G1032 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1056 removed outlier: 3.722A pdb=" N GLN G1056 " --> pdb=" O GLY G1052 " (cutoff:3.500A) Processing helix chain 'G' and resid 1059 through 1107 removed outlier: 3.991A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G1094 " --> pdb=" O GLU G1090 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1223 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.692A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 36 through 41 removed outlier: 4.101A pdb=" N PHE I 40 " --> pdb=" O GLN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 222 through 232 removed outlier: 4.065A pdb=" N TYR I 231 " --> pdb=" O SER I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 399 Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER I 435 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 453 removed outlier: 3.636A pdb=" N MET I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 529 removed outlier: 4.048A pdb=" N SER I 528 " --> pdb=" O PRO I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 805 through 812 Processing helix chain 'I' and resid 814 through 823 removed outlier: 3.791A pdb=" N GLU I 823 " --> pdb=" O GLN I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 826 through 854 removed outlier: 3.564A pdb=" N LYS I 830 " --> pdb=" O GLN I 826 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 915 removed outlier: 3.603A pdb=" N CYS I 912 " --> pdb=" O GLY I 908 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN I 914 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 940 through 954 removed outlier: 3.627A pdb=" N SER I 954 " --> pdb=" O SER I 950 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1007 Processing helix chain 'I' and resid 1008 through 1012 removed outlier: 4.413A pdb=" N PHE I1012 " --> pdb=" O GLN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 removed outlier: 3.597A pdb=" N LEU I1036 " --> pdb=" O ALA I1032 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1056 removed outlier: 3.821A pdb=" N GLN I1056 " --> pdb=" O GLY I1052 " (cutoff:3.500A) Processing helix chain 'I' and resid 1059 through 1107 removed outlier: 3.981A pdb=" N ALA I1065 " --> pdb=" O PRO I1061 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU I1094 " --> pdb=" O GLU I1090 " (cutoff:3.500A) Processing helix chain 'I' and resid 1219 through 1223 Processing helix chain 'J' and resid 36 through 41 removed outlier: 4.066A pdb=" N PHE J 40 " --> pdb=" O GLN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 222 through 232 removed outlier: 4.027A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 Processing helix chain 'J' and resid 411 through 416 Processing helix chain 'J' and resid 431 through 435 removed outlier: 3.704A pdb=" N SER J 435 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 453 removed outlier: 3.636A pdb=" N MET J 452 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 524 through 529 removed outlier: 3.735A pdb=" N SER J 528 " --> pdb=" O PRO J 525 " (cutoff:3.500A) Processing helix chain 'J' and resid 805 through 812 Processing helix chain 'J' and resid 814 through 823 removed outlier: 3.822A pdb=" N GLU J 823 " --> pdb=" O GLN J 819 " (cutoff:3.500A) Processing helix chain 'J' and resid 826 through 854 removed outlier: 3.654A pdb=" N LYS J 830 " --> pdb=" O GLN J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 888 through 898 Processing helix chain 'J' and resid 907 through 915 removed outlier: 3.936A pdb=" N GLN J 914 " --> pdb=" O ASP J 910 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 931 Processing helix chain 'J' and resid 940 through 953 Processing helix chain 'J' and resid 971 through 982 Processing helix chain 'J' and resid 986 through 993 Processing helix chain 'J' and resid 993 through 1007 Processing helix chain 'J' and resid 1008 through 1012 removed outlier: 4.467A pdb=" N PHE J1012 " --> pdb=" O GLN J1009 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1039 removed outlier: 3.630A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1050 through 1056 removed outlier: 3.670A pdb=" N GLN J1056 " --> pdb=" O GLY J1052 " (cutoff:3.500A) Processing helix chain 'J' and resid 1059 through 1107 removed outlier: 3.937A pdb=" N ALA J1065 " --> pdb=" O PRO J1061 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J1094 " --> pdb=" O GLU J1090 " (cutoff:3.500A) Processing helix chain 'J' and resid 1219 through 1223 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR A 94 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 152 removed outlier: 4.637A pdb=" N LEU A 148 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 187 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 150 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 185 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 152 " --> pdb=" O TYR A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.678A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 21 removed outlier: 3.796A pdb=" N ASP C 71 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER C 163 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR E 94 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AB6, first strand: chain 'E' and resid 148 through 152 removed outlier: 4.637A pdb=" N LEU E 148 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER E 187 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS E 150 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU E 185 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR E 152 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 160 Processing sheet with id=AB8, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 13 removed outlier: 5.677A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.796A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'F' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER F 163 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.431A pdb=" N HIS G 91 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 67 through 75 removed outlier: 4.302A pdb=" N ARG G 335 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.531A pdb=" N TYR G 314 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 263 " --> pdb=" O THR G 283 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR G 283 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU G 265 " --> pdb=" O PHE G 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 88 through 89 removed outlier: 7.322A pdb=" N SER G 88 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 206 " --> pdb=" O SER G 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AD1, first strand: chain 'G' and resid 127 through 129 removed outlier: 3.880A pdb=" N ALA G 309 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AD3, first strand: chain 'G' and resid 689 through 690 removed outlier: 5.499A pdb=" N VAL G 360 " --> pdb=" O TYR G 663 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR G 663 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER G 362 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL G 661 " --> pdb=" O SER G 362 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER G 364 " --> pdb=" O VAL G 659 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL G 659 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS G 713 " --> pdb=" O PHE G 674 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 373 through 376 removed outlier: 4.615A pdb=" N VAL G 639 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 631 " --> pdb=" O VAL G 639 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 400 through 404 removed outlier: 3.755A pdb=" N LYS G 400 " --> pdb=" O TYR G 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G 445 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 407 through 409 removed outlier: 6.704A pdb=" N CYS G 407 " --> pdb=" O CYS G 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 513 through 515 removed outlier: 3.699A pdb=" N TYR G 497 " --> pdb=" O VAL G 561 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER G 557 " --> pdb=" O ASN G 501 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 717 through 724 removed outlier: 6.738A pdb=" N VAL G 718 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N SER G 761 " --> pdb=" O VAL G 718 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N SER G 720 " --> pdb=" O SER G 761 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU G 735 " --> pdb=" O LEU G 731 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 768 through 769 removed outlier: 5.798A pdb=" N ILE G 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.073A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY G1188 " --> pdb=" O ALA G1193 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G1193 " --> pdb=" O GLY G1188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.073A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS G 779 " --> pdb=" O ALA I 969 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AE4, first strand: chain 'G' and resid 857 through 858 Processing sheet with id=AE5, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.302A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL J1124 " --> pdb=" O VAL J1139 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR J1141 " --> pdb=" O HIS J1122 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS J1122 " --> pdb=" O TYR J1141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.302A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL J1150 " --> pdb=" O LYS J1174 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE J1172 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY J1188 " --> pdb=" O ALA J1193 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA J1193 " --> pdb=" O GLY J1188 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.645A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AF1, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AF2, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.636A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 152 " --> pdb=" O TYR H 183 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 157 through 158 Processing sheet with id=AF4, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.413A pdb=" N HIS I 91 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 67 through 75 removed outlier: 4.234A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.312A pdb=" N VAL I 263 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR I 283 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU I 265 " --> pdb=" O PHE I 281 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AF8, first strand: chain 'I' and resid 127 through 129 removed outlier: 3.718A pdb=" N ALA I 309 " --> pdb=" O THR I 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AG1, first strand: chain 'I' and resid 206 through 208 removed outlier: 6.400A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'I' and resid 689 through 690 removed outlier: 4.542A pdb=" N VAL I 659 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER I 365 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL I 657 " --> pdb=" O SER I 365 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS I 713 " --> pdb=" O PHE I 674 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 372 through 376 removed outlier: 6.766A pdb=" N GLY I 372 " --> pdb=" O GLU I 605 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N SER I 607 " --> pdb=" O GLY I 372 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL I 374 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL I 631 " --> pdb=" O VAL I 639 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 400 through 404 removed outlier: 3.755A pdb=" N LYS I 400 " --> pdb=" O TYR I 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR I 445 " --> pdb=" O LYS I 400 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 407 through 409 Processing sheet with id=AG6, first strand: chain 'I' and resid 513 through 515 removed outlier: 3.700A pdb=" N TYR I 497 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER I 557 " --> pdb=" O ASN I 501 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 717 through 724 removed outlier: 6.707A pdb=" N VAL I 718 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N SER I 761 " --> pdb=" O VAL I 718 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N SER I 720 " --> pdb=" O SER I 761 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU I 735 " --> pdb=" O LEU I 731 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 768 through 769 removed outlier: 5.811A pdb=" N ILE I 768 " --> pdb=" O SER J 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA I1152 " --> pdb=" O TYR I 777 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR I 777 " --> pdb=" O ALA I1152 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS I 779 " --> pdb=" O ALA J 969 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AH3, first strand: chain 'I' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS I1164 " --> pdb=" O VAL I1205 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AH5, first strand: chain 'J' and resid 67 through 75 removed outlier: 4.296A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.528A pdb=" N TYR J 314 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL J 263 " --> pdb=" O THR J 283 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR J 283 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU J 265 " --> pdb=" O PHE J 281 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.291A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'J' and resid 110 through 111 Processing sheet with id=AH9, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.828A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AI2, first strand: chain 'J' and resid 689 through 690 removed outlier: 4.596A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 372 through 376 removed outlier: 3.906A pdb=" N GLY J 372 " --> pdb=" O CYS J 603 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.755A pdb=" N LYS J 400 " --> pdb=" O TYR J 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR J 445 " --> pdb=" O LYS J 400 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 408 through 409 Processing sheet with id=AI6, first strand: chain 'J' and resid 497 through 503 removed outlier: 3.701A pdb=" N TYR J 497 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER J 557 " --> pdb=" O ASN J 501 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 717 through 724 removed outlier: 6.728A pdb=" N VAL J 718 " --> pdb=" O LEU J 759 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N SER J 761 " --> pdb=" O VAL J 718 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N SER J 720 " --> pdb=" O SER J 761 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 802 through 804 Processing sheet with id=AI9, first strand: chain 'J' and resid 1202 through 1205 removed outlier: 4.167A pdb=" N CYS J1164 " --> pdb=" O VAL J1205 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 11 through 13 removed outlier: 5.676A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.796A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AJ4, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 154 through 155 1266 hydrogen bonds defined for protein. 3211 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: 18.89 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10725 1.33 - 1.46: 9041 1.46 - 1.59: 17960 1.59 - 1.71: 0 1.71 - 1.84: 240 Bond restraints: 37966 Sorted by residual: bond pdb=" C SER E 186 " pdb=" O SER E 186 " ideal model delta sigma weight residual 1.236 1.363 -0.127 1.21e-02 6.83e+03 1.11e+02 bond pdb=" C SER A 186 " pdb=" O SER A 186 " ideal model delta sigma weight residual 1.236 1.363 -0.127 1.21e-02 6.83e+03 1.10e+02 bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.21e-02 6.83e+03 1.09e+02 bond pdb=" C SER E 160 " pdb=" O SER E 160 " ideal model delta sigma weight residual 1.234 1.359 -0.124 1.22e-02 6.72e+03 1.04e+02 bond pdb=" C SER A 160 " pdb=" O SER A 160 " ideal model delta sigma weight residual 1.234 1.358 -0.124 1.22e-02 6.72e+03 1.03e+02 ... (remaining 37961 not shown) Histogram of bond angle deviations from ideal: 93.65 - 101.78: 73 101.78 - 109.91: 5721 109.91 - 118.05: 23311 118.05 - 126.18: 22088 126.18 - 134.31: 477 Bond angle restraints: 51670 Sorted by residual: angle pdb=" O SER A 186 " pdb=" C SER A 186 " pdb=" CA ASER A 186 " ideal model delta sigma weight residual 120.38 132.23 -11.85 1.09e+00 8.42e-01 1.18e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.21 -11.83 1.09e+00 8.42e-01 1.18e+02 angle pdb=" O SER E 186 " pdb=" C SER E 186 " pdb=" CA ASER E 186 " ideal model delta sigma weight residual 120.38 132.18 -11.80 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER A 186 " pdb=" C SER A 186 " pdb=" CA BSER A 186 " ideal model delta sigma weight residual 120.38 132.18 -11.80 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.17 -11.79 1.09e+00 8.42e-01 1.17e+02 ... (remaining 51665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19808 18.00 - 35.99: 2081 35.99 - 53.99: 621 53.99 - 71.98: 154 71.98 - 89.98: 72 Dihedral angle restraints: 22736 sinusoidal: 8667 harmonic: 14069 Sorted by residual: dihedral pdb=" CA GLY G 380 " pdb=" C GLY G 380 " pdb=" N VAL G 381 " pdb=" CA VAL G 381 " ideal model delta harmonic sigma weight residual -180.00 -137.64 -42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CB CYS I 176 " pdb=" SG CYS I 176 " pdb=" SG CYS I 214 " pdb=" CB CYS I 214 " ideal model delta sinusoidal sigma weight residual -86.00 -160.84 74.84 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CA GLU A 155 " pdb=" C GLU A 155 " pdb=" N PRO A 156 " pdb=" CA PRO A 156 " ideal model delta harmonic sigma weight residual 0.00 41.03 -41.03 0 5.00e+00 4.00e-02 6.74e+01 ... (remaining 22733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4816 0.084 - 0.168: 835 0.168 - 0.251: 146 0.251 - 0.335: 8 0.335 - 0.419: 8 Chirality restraints: 5813 Sorted by residual: chirality pdb=" CA GLN H 199 " pdb=" N GLN H 199 " pdb=" C GLN H 199 " pdb=" CB GLN H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ALA E 24 " pdb=" N ALA E 24 " pdb=" C ALA E 24 " pdb=" CB ALA E 24 " both_signs ideal model delta sigma weight residual False 2.48 2.85 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA BSER E 186 " pdb=" N SER E 186 " pdb=" C SER E 186 " pdb=" CB BSER E 186 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 5810 not shown) Planarity restraints: 6698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 22 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C CYS E 22 " 0.079 2.00e-02 2.50e+03 pdb=" O CYS E 22 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS E 23 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 377 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN I 377 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN I 377 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA I 378 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 91 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C GLN K 91 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN K 91 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR K 92 " 0.015 2.00e-02 2.50e+03 ... (remaining 6695 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 4 1.82 - 2.59: 319 2.59 - 3.36: 45305 3.36 - 4.13: 89421 4.13 - 4.90: 161714 Nonbonded interactions: 296763 Sorted by model distance: nonbonded pdb=" OE2 GLU I 376 " pdb=" NZ LYS I 595 " model vdw 1.050 2.520 nonbonded pdb=" OD2 ASP I 580 " pdb=" NH2 ARG J 62 " model vdw 1.593 2.520 nonbonded pdb=" O SER E 75 " pdb=" OG SER H 168 " model vdw 1.655 2.440 nonbonded pdb=" SG CYS I 437 " pdb=" CA GLY I 610 " model vdw 1.700 3.800 nonbonded pdb=" O SER E 75 " pdb=" CB SER H 168 " model vdw 2.037 3.440 ... (remaining 296758 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' and (resid 3 through 25 or resid 32 through 159 or resid 167 through \ 185 or resid 187 through 221)) selection = (chain 'E' and (resid 3 through 159 or resid 167 through 185 or resid 187 throug \ h 221)) selection = (chain 'H' and (resid 3 through 25 or resid 32 through 159 or resid 167 through \ 185 or resid 187 through 221)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'K' } ncs_group { reference = (chain 'G' and (resid 18 through 507 or resid 516 through 1223)) selection = (chain 'I' and (resid 18 through 507 or resid 516 through 1223)) selection = chain 'J' } 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=0.40 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.030 Extract box with map and model: 8.910 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 97.230 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.190 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:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3139 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 0.127 37966 Z= 0.505 Angle : 1.079 17.351 51670 Z= 0.723 Chirality : 0.065 0.419 5813 Planarity : 0.005 0.058 6698 Dihedral : 17.292 89.977 13578 Min Nonbonded Distance : 1.050 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 1.08 % Allowed : 10.34 % Favored : 88.58 % Rotamer: Outliers : 9.22 % Allowed : 16.93 % Favored : 73.85 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.13 % Twisted Proline : 1.21 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.12), residues: 4813 helix: 1.08 (0.21), residues: 683 sheet: -1.21 (0.14), residues: 1331 loop : -2.06 (0.11), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.007 0.001 HIS G 194 PHE 0.022 0.002 PHE G 156 TYR 0.031 0.002 TYR J 438 ARG 0.011 0.001 ARG G 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 381 poor density : 699 time to evaluate : 4.015 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: E 214 VAL cc_start: 0.5733 (t) cc_final: 0.5456 (t) REVERT: F 39 GLN cc_start: 0.1644 (pt0) cc_final: 0.1201 (tm-30) REVERT: G 25 SER cc_start: -0.2115 (OUTLIER) cc_final: -0.2478 (t) REVERT: G 102 VAL cc_start: 0.0841 (OUTLIER) cc_final: 0.0632 (m) REVERT: G 294 SER cc_start: 0.2380 (OUTLIER) cc_final: 0.0446 (m) REVERT: G 871 LEU cc_start: 0.1244 (OUTLIER) cc_final: 0.0830 (pp) REVERT: G 1175 THR cc_start: 0.0480 (OUTLIER) cc_final: -0.1352 (t) REVERT: I 704 TYR cc_start: 0.2606 (OUTLIER) cc_final: 0.2318 (p90) REVERT: I 910 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.4988 (m-30) REVERT: J 228 PHE cc_start: 0.4833 (t80) cc_final: 0.4322 (t80) REVERT: J 256 ILE cc_start: 0.7865 (tt) cc_final: 0.7641 (pp) REVERT: J 361 TYR cc_start: 0.6122 (m-80) cc_final: 0.5813 (m-80) REVERT: J 373 SER cc_start: 0.1379 (OUTLIER) cc_final: 0.1108 (t) REVERT: J 856 SER cc_start: -0.1851 (OUTLIER) cc_final: -0.2635 (p) REVERT: J 910 ASP cc_start: 0.1049 (OUTLIER) cc_final: 0.0651 (p0) REVERT: J 1209 VAL cc_start: 0.2272 (OUTLIER) cc_final: 0.1759 (m) REVERT: K 198 THR cc_start: 0.4104 (OUTLIER) cc_final: 0.3669 (p) outliers start: 381 outliers final: 59 residues processed: 1020 average time/residue: 0.9835 time to fit residues: 1304.8757 Evaluate side-chains 458 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 387 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 ASP Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 422 ASP Chi-restraints excluded: chain G residue 604 VAL Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 781 SER Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1095 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1216 THR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 720 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 910 ASP Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1089 SER Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 829 SER Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 890 ILE Chi-restraints excluded: chain J residue 910 ASP Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1216 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 3.9990 chunk 364 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 377 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 436 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 162 ASN A 178 GLN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 43 GLN E 6 GLN E 171 HIS E 178 GLN F 101 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 ASN G 521 ASN G 592 ASN G 819 GLN G1110 GLN G1129 ASN G1146 HIS H 6 GLN ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN I 244 ASN I1023 GLN I1056 GLN I1072 ASN ** I1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1208 GLN J 521 ASN J 628 GLN J 800 GLN J 812 ASN J 819 GLN J 836 HIS J1129 ASN J1146 HIS J1212 GLN K 91 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4033 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37966 Z= 0.318 Angle : 0.866 14.357 51670 Z= 0.443 Chirality : 0.050 0.243 5813 Planarity : 0.006 0.075 6698 Dihedral : 6.903 55.634 5355 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.84 % Favored : 91.91 % Rotamer: Outliers : 6.41 % Allowed : 22.57 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.11), residues: 4813 helix: 0.55 (0.19), residues: 728 sheet: -1.02 (0.13), residues: 1354 loop : -1.97 (0.11), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP E 47 HIS 0.016 0.002 HIS G1138 PHE 0.028 0.003 PHE K 99 TYR 0.035 0.002 TYR C 92 ARG 0.012 0.001 ARG J 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 438 time to evaluate : 3.878 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: C 197 VAL cc_start: 0.2938 (OUTLIER) cc_final: 0.2725 (p) REVERT: G 31 ILE cc_start: 0.0190 (OUTLIER) cc_final: -0.0450 (pp) REVERT: G 523 TYR cc_start: 0.4002 (OUTLIER) cc_final: 0.1781 (m-80) REVERT: G 906 MET cc_start: 0.3899 (ttp) cc_final: 0.3625 (ttp) REVERT: G 1175 THR cc_start: 0.0714 (OUTLIER) cc_final: -0.1006 (t) REVERT: I 203 SER cc_start: 0.0738 (OUTLIER) cc_final: 0.0397 (p) REVERT: I 234 LEU cc_start: 0.3993 (OUTLIER) cc_final: 0.3748 (mm) REVERT: I 641 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4728 (t80) REVERT: I 704 TYR cc_start: 0.2681 (OUTLIER) cc_final: 0.1712 (p90) REVERT: I 717 LEU cc_start: 0.2388 (OUTLIER) cc_final: 0.1876 (tm) REVERT: I 906 MET cc_start: 0.5064 (OUTLIER) cc_final: 0.4848 (tpp) REVERT: J 164 PHE cc_start: 0.4593 (m-10) cc_final: 0.4391 (m-10) REVERT: J 303 ILE cc_start: 0.6654 (mm) cc_final: 0.6407 (mm) REVERT: J 816 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7673 (tppp) REVERT: J 820 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8753 (mt) REVERT: J 840 LEU cc_start: 0.8060 (tt) cc_final: 0.7740 (tp) REVERT: J 1146 HIS cc_start: 0.2033 (p90) cc_final: 0.1317 (m-70) outliers start: 265 outliers final: 79 residues processed: 642 average time/residue: 1.0077 time to fit residues: 841.4120 Evaluate side-chains 402 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 311 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 523 TYR Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 673 LEU Chi-restraints excluded: chain G residue 771 ASP Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 1087 VAL Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 438 TYR Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 641 TYR Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 803 THR Chi-restraints excluded: chain I residue 804 VAL Chi-restraints excluded: chain I residue 856 SER Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 906 MET Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1209 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 227 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 816 LYS Chi-restraints excluded: chain J residue 820 LEU Chi-restraints excluded: chain J residue 965 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 242 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 437 optimal weight: 0.8980 chunk 472 optimal weight: 1.9990 chunk 389 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 351 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 43 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN G 280 GLN G 566 GLN G 815 GLN G 819 GLN G1110 GLN ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 HIS ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1122 HIS ** I1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 522 GLN J 566 GLN ** J 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 808 GLN ** J1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4585 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 37966 Z= 0.297 Angle : 0.780 14.579 51670 Z= 0.405 Chirality : 0.049 0.398 5813 Planarity : 0.005 0.101 6698 Dihedral : 5.656 57.859 5275 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.65 % Favored : 92.05 % Rotamer: Outliers : 6.05 % Allowed : 23.83 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 4813 helix: 0.67 (0.20), residues: 720 sheet: -1.03 (0.13), residues: 1366 loop : -1.89 (0.11), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 47 HIS 0.014 0.002 HIS E 171 PHE 0.025 0.002 PHE C 99 TYR 0.024 0.002 TYR H 183 ARG 0.021 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 398 time to evaluate : 3.999 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: A 50 ARG cc_start: 0.3583 (pmt-80) cc_final: 0.3287 (ttp80) REVERT: C 118 ILE cc_start: 0.0662 (OUTLIER) cc_final: 0.0351 (mm) REVERT: G 523 TYR cc_start: 0.3765 (OUTLIER) cc_final: 0.1905 (m-80) REVERT: G 686 MET cc_start: 0.7874 (mmp) cc_final: 0.7578 (mmm) REVERT: G 871 LEU cc_start: -0.0265 (OUTLIER) cc_final: -0.0661 (pp) REVERT: G 1103 VAL cc_start: 0.1438 (OUTLIER) cc_final: 0.1128 (t) REVERT: G 1175 THR cc_start: 0.0560 (OUTLIER) cc_final: -0.0252 (m) REVERT: I 132 ILE cc_start: 0.2958 (OUTLIER) cc_final: 0.2508 (mp) REVERT: I 203 SER cc_start: 0.1269 (OUTLIER) cc_final: 0.1040 (p) REVERT: I 234 LEU cc_start: 0.4322 (OUTLIER) cc_final: 0.4037 (mm) REVERT: I 246 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8079 (m) REVERT: I 310 TRP cc_start: 0.5711 (m-10) cc_final: 0.5336 (m-10) REVERT: I 641 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5888 (t80) REVERT: I 729 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7959 (mm) REVERT: I 861 ILE cc_start: 0.1264 (OUTLIER) cc_final: 0.1040 (pp) REVERT: I 1180 ILE cc_start: -0.0337 (OUTLIER) cc_final: -0.0797 (tt) REVERT: J 167 HIS cc_start: 0.5328 (OUTLIER) cc_final: 0.4977 (t-170) REVERT: J 228 PHE cc_start: 0.7396 (t80) cc_final: 0.7139 (t80) REVERT: J 233 ASN cc_start: 0.5985 (m-40) cc_final: 0.5720 (m110) REVERT: J 291 LYS cc_start: 0.7831 (mppt) cc_final: 0.7493 (mppt) REVERT: J 710 PRO cc_start: 0.4065 (Cg_exo) cc_final: 0.3222 (Cg_endo) REVERT: J 816 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8080 (tppp) REVERT: J 1218 LEU cc_start: -0.0839 (OUTLIER) cc_final: -0.1058 (tt) REVERT: K 198 THR cc_start: 0.5911 (OUTLIER) cc_final: 0.5296 (p) outliers start: 250 outliers final: 78 residues processed: 589 average time/residue: 1.0596 time to fit residues: 812.4287 Evaluate side-chains 385 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 290 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 523 TYR Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 714 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 910 ASP Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 641 TYR Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 660 SER Chi-restraints excluded: chain I residue 729 LEU Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 856 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1125 SER Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1198 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 446 PHE Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 635 TYR Chi-restraints excluded: chain J residue 650 CYS Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 816 LYS Chi-restraints excluded: chain J residue 844 ASP Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1218 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 211 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 208 optimal weight: 0.5980 chunk 293 optimal weight: 0.5980 chunk 439 optimal weight: 1.9990 chunk 464 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 416 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN E 162 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN G1110 GLN H 39 GLN ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN I 408 ASN I 486 HIS I 981 ASN I1042 ASN ** I1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1129 ASN ** J 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN J 398 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 808 GLN J1016 ASN K 161 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37966 Z= 0.216 Angle : 0.700 11.924 51670 Z= 0.357 Chirality : 0.045 0.356 5813 Planarity : 0.005 0.077 6698 Dihedral : 5.233 51.282 5267 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.15 % Favored : 92.57 % Rotamer: Outliers : 4.67 % Allowed : 26.32 % Favored : 69.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4813 helix: 0.66 (0.20), residues: 744 sheet: -0.82 (0.14), residues: 1359 loop : -1.93 (0.11), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 47 HIS 0.008 0.001 HIS J1138 PHE 0.022 0.002 PHE J 571 TYR 0.048 0.002 TYR J1135 ARG 0.014 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 342 time to evaluate : 3.991 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: C 91 GLN cc_start: 0.0232 (tt0) cc_final: -0.0157 (tm130) REVERT: G 31 ILE cc_start: 0.0393 (OUTLIER) cc_final: -0.0327 (pp) REVERT: G 256 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5042 (mt) REVERT: G 563 MET cc_start: 0.2726 (tpt) cc_final: 0.2455 (tpt) REVERT: G 686 MET cc_start: 0.8090 (mmp) cc_final: 0.7839 (mmm) REVERT: G 801 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8642 (mtmt) REVERT: G 871 LEU cc_start: 0.0004 (OUTLIER) cc_final: -0.0270 (pp) REVERT: G 1090 GLU cc_start: 0.7755 (tp30) cc_final: 0.7494 (tp30) REVERT: I 132 ILE cc_start: 0.3196 (OUTLIER) cc_final: 0.2855 (mp) REVERT: I 240 MET cc_start: 0.0330 (tpp) cc_final: -0.1830 (ptm) REVERT: I 246 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8215 (m) REVERT: I 686 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4493 (mpt) REVERT: I 939 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6318 (mtm) REVERT: J 167 HIS cc_start: 0.5172 (OUTLIER) cc_final: 0.4891 (t-170) REVERT: J 228 PHE cc_start: 0.7322 (t80) cc_final: 0.7109 (t80) REVERT: J 233 ASN cc_start: 0.5847 (m-40) cc_final: 0.5538 (m110) REVERT: J 235 ARG cc_start: 0.6331 (mmp80) cc_final: 0.6053 (mmp80) REVERT: J 289 THR cc_start: 0.8384 (m) cc_final: 0.8176 (m) REVERT: J 291 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7482 (mppt) REVERT: J 629 ARG cc_start: 0.2033 (OUTLIER) cc_final: 0.1471 (ptm160) REVERT: J 816 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8211 (tppp) REVERT: J 943 MET cc_start: 0.6992 (tpp) cc_final: 0.6661 (tpp) REVERT: J 1008 MET cc_start: 0.4457 (mmp) cc_final: 0.3899 (mmm) REVERT: J 1103 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6607 (t) REVERT: K 155 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.2972 (mt) outliers start: 193 outliers final: 77 residues processed: 490 average time/residue: 1.0691 time to fit residues: 678.0347 Evaluate side-chains 387 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 296 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain G residue 692 SER Chi-restraints excluded: chain G residue 714 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 801 LYS Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 686 MET Chi-restraints excluded: chain I residue 709 THR Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 791 THR Chi-restraints excluded: chain I residue 795 ILE Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 888 SER Chi-restraints excluded: chain I residue 939 MET Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1051 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1125 SER Chi-restraints excluded: chain I residue 1198 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 291 LYS Chi-restraints excluded: chain J residue 446 PHE Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 629 ARG Chi-restraints excluded: chain J residue 635 TYR Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 816 LYS Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 890 ILE Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 1103 VAL Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 346 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 396 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 237 optimal weight: 6.9990 chunk 417 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN ** G 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN G 566 GLN ** G 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 848 ASN G 999 ASN G1020 GLN ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1145 ASN H 6 GLN ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS I 566 GLN ** I 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 836 HIS ** I1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 HIS ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN J 167 HIS ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 522 GLN ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 GLN J 800 GLN J 808 GLN ** J 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 994 GLN J1029 ASN J1129 ASN J1160 ASN J1212 GLN J1213 ASN K 153 ASN K 161 GLN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.9756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 37966 Z= 0.393 Angle : 0.880 13.156 51670 Z= 0.462 Chirality : 0.053 0.356 5813 Planarity : 0.006 0.086 6698 Dihedral : 6.126 50.466 5266 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.99 % Favored : 90.70 % Rotamer: Outliers : 6.34 % Allowed : 25.64 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 4813 helix: -0.10 (0.19), residues: 743 sheet: -0.88 (0.14), residues: 1260 loop : -2.19 (0.11), residues: 2810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP E 47 HIS 0.013 0.002 HIS J1138 PHE 0.051 0.003 PHE J 778 TYR 0.064 0.003 TYR J1135 ARG 0.045 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 374 time to evaluate : 4.087 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: C 27 GLN cc_start: -0.0730 (pp30) cc_final: -0.1212 (pp30) REVERT: C 91 GLN cc_start: 0.0048 (tt0) cc_final: -0.0358 (tm130) REVERT: G 183 PHE cc_start: 0.5206 (OUTLIER) cc_final: 0.4807 (p90) REVERT: G 277 ASN cc_start: 0.6711 (OUTLIER) cc_final: 0.6484 (t0) REVERT: G 314 TYR cc_start: 0.3222 (OUTLIER) cc_final: 0.2304 (m-80) REVERT: G 719 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7048 (m-40) REVERT: G 771 ASP cc_start: 0.4382 (OUTLIER) cc_final: 0.3519 (m-30) REVERT: G 913 MET cc_start: 0.7852 (tpt) cc_final: 0.7635 (tpp) REVERT: G 955 ILE cc_start: -0.1311 (OUTLIER) cc_final: -0.1529 (mt) REVERT: G 1141 TYR cc_start: -0.0598 (OUTLIER) cc_final: -0.1495 (t80) REVERT: G 1174 LYS cc_start: 0.2633 (OUTLIER) cc_final: 0.1880 (mmmt) REVERT: G 1185 SER cc_start: 0.0667 (OUTLIER) cc_final: 0.0231 (p) REVERT: H 67 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6496 (ptm160) REVERT: I 240 MET cc_start: 0.4923 (tpp) cc_final: 0.4322 (tpp) REVERT: I 841 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7806 (mtm110) REVERT: I 906 MET cc_start: 0.6624 (tmm) cc_final: 0.6278 (ttt) REVERT: I 985 ILE cc_start: 0.0939 (OUTLIER) cc_final: 0.0601 (tp) REVERT: I 999 ASN cc_start: 0.4016 (m-40) cc_final: 0.3434 (m-40) REVERT: I 1180 ILE cc_start: -0.0327 (OUTLIER) cc_final: -0.0752 (tt) REVERT: J 155 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7257 (m-40) REVERT: J 291 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8153 (mmmm) REVERT: J 807 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8846 (ttpp) REVERT: J 840 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9035 (mp) REVERT: J 862 ILE cc_start: -0.2144 (OUTLIER) cc_final: -0.2649 (pp) REVERT: J 910 ASP cc_start: 0.5999 (m-30) cc_final: 0.5633 (m-30) REVERT: J 1210 THR cc_start: 0.1389 (OUTLIER) cc_final: 0.0886 (p) REVERT: K 155 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4257 (mp) outliers start: 262 outliers final: 87 residues processed: 582 average time/residue: 1.0476 time to fit residues: 785.1997 Evaluate side-chains 401 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 294 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 277 ASN Chi-restraints excluded: chain G residue 314 TYR Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 446 PHE Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 571 PHE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 719 ASN Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 771 ASP Chi-restraints excluded: chain G residue 801 LYS Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 955 ILE Chi-restraints excluded: chain G residue 1141 TYR Chi-restraints excluded: chain G residue 1174 LYS Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1185 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 438 TYR Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 873 LEU Chi-restraints excluded: chain I residue 923 LEU Chi-restraints excluded: chain I residue 943 MET Chi-restraints excluded: chain I residue 985 ILE Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1198 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 291 LYS Chi-restraints excluded: chain J residue 396 VAL Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 643 SER Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 807 LYS Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 947 TYR Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1210 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 156 optimal weight: 0.9990 chunk 418 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 465 optimal weight: 0.0010 chunk 386 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 chunk 38 optimal weight: 50.0000 chunk 153 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN G 91 HIS G 277 ASN G 592 ASN G 999 ASN G1110 GLN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 566 GLN I 819 GLN I1097 GLN ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1145 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 0.9927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37966 Z= 0.198 Angle : 0.704 14.916 51670 Z= 0.356 Chirality : 0.045 0.345 5813 Planarity : 0.005 0.113 6698 Dihedral : 5.363 50.627 5263 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.26 % Favored : 92.47 % Rotamer: Outliers : 3.51 % Allowed : 29.27 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.12), residues: 4813 helix: 0.49 (0.19), residues: 765 sheet: -0.79 (0.14), residues: 1327 loop : -2.01 (0.11), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 47 HIS 0.024 0.001 HIS I 486 PHE 0.031 0.002 PHE G 571 TYR 0.031 0.002 TYR A 32 ARG 0.009 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 317 time to evaluate : 4.169 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: C 91 GLN cc_start: 0.0368 (tt0) cc_final: -0.0013 (tm130) REVERT: C 118 ILE cc_start: 0.0771 (OUTLIER) cc_final: 0.0426 (mm) REVERT: G 31 ILE cc_start: 0.0646 (OUTLIER) cc_final: -0.0251 (pp) REVERT: G 563 MET cc_start: 0.3069 (OUTLIER) cc_final: 0.2005 (tpt) REVERT: G 771 ASP cc_start: 0.3607 (OUTLIER) cc_final: 0.2904 (m-30) REVERT: G 924 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7147 (mt) REVERT: G 1173 ILE cc_start: 0.2658 (OUTLIER) cc_final: 0.1330 (tp) REVERT: H 29 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6493 (t80) REVERT: H 206 ASN cc_start: 0.6044 (OUTLIER) cc_final: 0.5797 (p0) REVERT: I 240 MET cc_start: 0.5174 (tpp) cc_final: 0.4915 (tpp) REVERT: I 686 MET cc_start: 0.8001 (mmm) cc_final: 0.7774 (mmm) REVERT: I 906 MET cc_start: 0.6862 (tmm) cc_final: 0.6481 (ttt) REVERT: J 235 ARG cc_start: 0.7331 (mmp80) cc_final: 0.7114 (mmp80) REVERT: J 292 TYR cc_start: 0.8339 (m-80) cc_final: 0.7990 (m-80) REVERT: J 295 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7907 (mp) REVERT: J 734 SER cc_start: 0.7329 (m) cc_final: 0.6803 (t) REVERT: J 859 SER cc_start: 0.1435 (OUTLIER) cc_final: 0.1021 (m) REVERT: J 862 ILE cc_start: -0.1155 (OUTLIER) cc_final: -0.1641 (pp) REVERT: J 1053 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: K 198 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6577 (p) outliers start: 145 outliers final: 56 residues processed: 427 average time/residue: 1.1090 time to fit residues: 608.0658 Evaluate side-chains 338 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 269 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 423 PHE Chi-restraints excluded: chain G residue 446 PHE Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 563 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 771 ASP Chi-restraints excluded: chain G residue 924 ILE Chi-restraints excluded: chain G residue 1173 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 1162 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 844 ASP Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1053 ASP Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 448 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 265 optimal weight: 0.0070 chunk 339 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 GLN G1138 HIS H 206 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 993 ASN ** J1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1160 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 1.0258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 37966 Z= 0.205 Angle : 0.682 13.525 51670 Z= 0.346 Chirality : 0.045 0.401 5813 Planarity : 0.005 0.065 6698 Dihedral : 5.185 56.683 5262 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.05 % Favored : 91.68 % Rotamer: Outliers : 3.19 % Allowed : 29.32 % Favored : 67.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.12), residues: 4813 helix: 0.82 (0.20), residues: 750 sheet: -0.76 (0.14), residues: 1333 loop : -1.91 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP E 47 HIS 0.014 0.001 HIS H 207 PHE 0.087 0.002 PHE G 423 TYR 0.032 0.001 TYR F 88 ARG 0.008 0.001 ARG I 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 309 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLN cc_start: 0.0159 (tt0) cc_final: -0.0263 (tm130) REVERT: C 118 ILE cc_start: 0.0622 (OUTLIER) cc_final: 0.0293 (mm) REVERT: F 39 GLN cc_start: 0.1959 (OUTLIER) cc_final: 0.1512 (tp40) REVERT: G 31 ILE cc_start: 0.0606 (OUTLIER) cc_final: -0.0269 (pp) REVERT: G 84 MET cc_start: 0.5528 (tpt) cc_final: 0.5162 (tpt) REVERT: G 240 MET cc_start: 0.6553 (mmm) cc_final: 0.6327 (mpt) REVERT: G 343 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: G 563 MET cc_start: 0.2896 (OUTLIER) cc_final: 0.2004 (tpt) REVERT: G 924 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7253 (mt) REVERT: G 1173 ILE cc_start: 0.2552 (OUTLIER) cc_final: 0.1372 (tp) REVERT: H 29 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6505 (t80) REVERT: I 240 MET cc_start: 0.5542 (tpp) cc_final: 0.5225 (tpp) REVERT: I 259 THR cc_start: 0.8372 (p) cc_final: 0.8057 (p) REVERT: I 906 MET cc_start: 0.6915 (tmm) cc_final: 0.6549 (ttt) REVERT: I 1180 ILE cc_start: -0.0301 (OUTLIER) cc_final: -0.0661 (tt) REVERT: J 235 ARG cc_start: 0.7193 (mmp80) cc_final: 0.6946 (mmp80) REVERT: J 240 MET cc_start: 0.8450 (tmt) cc_final: 0.8149 (tmt) REVERT: J 288 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7258 (p0) REVERT: J 289 THR cc_start: 0.8882 (m) cc_final: 0.8464 (t) REVERT: J 292 TYR cc_start: 0.8397 (m-80) cc_final: 0.8034 (m-80) REVERT: J 295 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7937 (mp) REVERT: J 734 SER cc_start: 0.7138 (m) cc_final: 0.6609 (t) REVERT: K 155 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.5027 (mt) REVERT: K 198 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6645 (p) outliers start: 132 outliers final: 69 residues processed: 410 average time/residue: 1.0800 time to fit residues: 571.3229 Evaluate side-chains 351 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 269 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 563 MET Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 924 ILE Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1173 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 438 TYR Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1162 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 328 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 286 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 43 optimal weight: 40.0000 chunk 364 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS C 39 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 GLN G 808 GLN G 999 ASN G1023 GLN ** G1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1132 ASN ** G1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN I 486 HIS I 769 GLN ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 1.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 37966 Z= 0.341 Angle : 0.826 19.507 51670 Z= 0.423 Chirality : 0.050 0.467 5813 Planarity : 0.006 0.096 6698 Dihedral : 5.931 54.305 5261 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.62 % Rotamer: Outliers : 3.87 % Allowed : 28.81 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.12), residues: 4813 helix: 0.31 (0.19), residues: 762 sheet: -0.85 (0.15), residues: 1278 loop : -2.03 (0.11), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP C 36 HIS 0.013 0.002 HIS J1138 PHE 0.048 0.003 PHE J1126 TYR 0.048 0.002 TYR G 314 ARG 0.018 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 315 time to evaluate : 4.084 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: C 27 GLN cc_start: -0.0772 (OUTLIER) cc_final: -0.1363 (pp30) REVERT: C 91 GLN cc_start: 0.0150 (tt0) cc_final: -0.0269 (tm130) REVERT: C 118 ILE cc_start: 0.0718 (OUTLIER) cc_final: 0.0372 (mm) REVERT: E 145 LEU cc_start: 0.3181 (pt) cc_final: 0.2746 (mp) REVERT: G 31 ILE cc_start: 0.1166 (OUTLIER) cc_final: 0.0520 (pt) REVERT: G 143 ILE cc_start: 0.6726 (tp) cc_final: 0.6329 (tt) REVERT: G 314 TYR cc_start: 0.4372 (OUTLIER) cc_final: 0.3714 (m-80) REVERT: G 563 MET cc_start: 0.3193 (OUTLIER) cc_final: 0.2408 (tpt) REVERT: G 771 ASP cc_start: 0.4993 (OUTLIER) cc_final: 0.4406 (m-30) REVERT: H 29 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6787 (t80) REVERT: I 133 SER cc_start: 0.8452 (t) cc_final: 0.8214 (t) REVERT: I 184 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: I 259 THR cc_start: 0.8449 (p) cc_final: 0.8174 (p) REVERT: J 84 MET cc_start: 0.8632 (ttp) cc_final: 0.8410 (ttp) REVERT: J 184 TYR cc_start: 0.5335 (OUTLIER) cc_final: 0.4779 (m-10) REVERT: J 240 MET cc_start: 0.8418 (tmt) cc_final: 0.8091 (tmt) REVERT: J 734 SER cc_start: 0.7186 (m) cc_final: 0.6626 (t) REVERT: J 862 ILE cc_start: -0.0652 (OUTLIER) cc_final: -0.1292 (tt) REVERT: J 1053 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: J 1211 TYR cc_start: 0.4613 (m-10) cc_final: 0.4340 (m-10) REVERT: K 159 ASN cc_start: 0.6959 (p0) cc_final: 0.5926 (m110) outliers start: 160 outliers final: 73 residues processed: 435 average time/residue: 1.1513 time to fit residues: 636.6090 Evaluate side-chains 363 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 279 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 87 TYR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 314 TYR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 424 THR Chi-restraints excluded: chain G residue 446 PHE Chi-restraints excluded: chain G residue 467 PHE Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 563 MET Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 771 ASP Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 438 TYR Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 873 LEU Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1162 THR Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1053 ASP Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain J residue 1151 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 421 optimal weight: 3.9990 chunk 444 optimal weight: 0.8980 chunk 405 optimal weight: 1.9990 chunk 432 optimal weight: 0.7980 chunk 260 optimal weight: 0.3980 chunk 188 optimal weight: 5.9990 chunk 339 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 390 optimal weight: 8.9990 chunk 408 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN E 62 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 808 GLN G 999 ASN G1023 GLN ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1110 GLN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN I1020 GLN J 194 HIS J 636 GLN J 907 GLN J 993 ASN ** J1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1208 GLN K 38 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 1.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 37966 Z= 0.214 Angle : 0.713 13.117 51670 Z= 0.361 Chirality : 0.046 0.414 5813 Planarity : 0.005 0.064 6698 Dihedral : 5.435 55.966 5259 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.86 % Favored : 91.93 % Rotamer: Outliers : 2.52 % Allowed : 30.43 % Favored : 67.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4813 helix: 0.67 (0.20), residues: 757 sheet: -0.75 (0.14), residues: 1278 loop : -1.91 (0.11), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP E 47 HIS 0.037 0.001 HIS I 486 PHE 0.028 0.002 PHE J 788 TYR 0.032 0.002 TYR G 314 ARG 0.012 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 288 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLN cc_start: 0.0304 (tt0) cc_final: -0.0011 (tm-30) REVERT: C 118 ILE cc_start: 0.0492 (OUTLIER) cc_final: 0.0127 (mm) REVERT: G 31 ILE cc_start: 0.1287 (OUTLIER) cc_final: 0.0644 (pt) REVERT: G 47 PRO cc_start: 0.6440 (Cg_exo) cc_final: 0.6148 (Cg_endo) REVERT: G 143 ILE cc_start: 0.6861 (tp) cc_final: 0.6493 (tt) REVERT: G 148 MET cc_start: 0.6642 (tmm) cc_final: 0.5384 (ptt) REVERT: G 163 ARG cc_start: 0.2517 (OUTLIER) cc_final: 0.1535 (ttt180) REVERT: G 343 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: G 563 MET cc_start: 0.2870 (OUTLIER) cc_final: 0.2170 (tpt) REVERT: G 700 ARG cc_start: 0.5918 (ptt180) cc_final: 0.5589 (ptt-90) REVERT: I 133 SER cc_start: 0.8658 (t) cc_final: 0.8421 (t) REVERT: I 259 THR cc_start: 0.8474 (p) cc_final: 0.8218 (p) REVERT: J 184 TYR cc_start: 0.5193 (OUTLIER) cc_final: 0.4596 (m-10) REVERT: J 235 ARG cc_start: 0.7962 (mmp80) cc_final: 0.7713 (mmp-170) REVERT: J 240 MET cc_start: 0.8303 (tmt) cc_final: 0.7927 (tmt) REVERT: J 289 THR cc_start: 0.8976 (m) cc_final: 0.8638 (t) REVERT: J 292 TYR cc_start: 0.8477 (m-80) cc_final: 0.8203 (m-80) REVERT: J 734 SER cc_start: 0.7033 (m) cc_final: 0.6509 (t) REVERT: J 862 ILE cc_start: -0.0142 (OUTLIER) cc_final: -0.0477 (tt) REVERT: J 1211 TYR cc_start: 0.4382 (m-10) cc_final: 0.3798 (m-10) REVERT: K 159 ASN cc_start: 0.6795 (p0) cc_final: 0.5718 (m110) outliers start: 104 outliers final: 49 residues processed: 369 average time/residue: 1.1283 time to fit residues: 533.9843 Evaluate side-chains 318 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 423 PHE Chi-restraints excluded: chain G residue 563 MET Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1162 THR Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1108 LYS Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 283 optimal weight: 4.9990 chunk 456 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 216 optimal weight: 0.0030 chunk 317 optimal weight: 1.9990 chunk 479 optimal weight: 9.9990 chunk 441 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 39 optimal weight: 0.0010 chunk 294 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN I 766 HIS I 819 GLN ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN J 981 ASN J 993 ASN ** J1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1208 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 1.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 37966 Z= 0.250 Angle : 0.731 13.589 51670 Z= 0.373 Chirality : 0.047 0.391 5813 Planarity : 0.005 0.060 6698 Dihedral : 5.466 59.025 5259 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.44 % Favored : 91.35 % Rotamer: Outliers : 1.91 % Allowed : 31.18 % Favored : 66.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4813 helix: 0.67 (0.20), residues: 752 sheet: -0.74 (0.14), residues: 1274 loop : -1.87 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 47 HIS 0.008 0.001 HIS J1122 PHE 0.073 0.002 PHE G 423 TYR 0.045 0.002 TYR G 314 ARG 0.013 0.001 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 295 time to evaluate : 4.184 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: C 91 GLN cc_start: 0.0275 (tt0) cc_final: -0.0013 (tm130) REVERT: C 118 ILE cc_start: 0.0435 (OUTLIER) cc_final: 0.0080 (mm) REVERT: E 48 MET cc_start: 0.2545 (OUTLIER) cc_final: 0.2100 (mmp) REVERT: G 31 ILE cc_start: 0.1504 (OUTLIER) cc_final: 0.0915 (pt) REVERT: G 143 ILE cc_start: 0.7093 (tp) cc_final: 0.6843 (tt) REVERT: G 163 ARG cc_start: 0.2915 (OUTLIER) cc_final: 0.1974 (ttt180) REVERT: G 333 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7766 (mt) REVERT: G 343 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: G 563 MET cc_start: 0.2939 (OUTLIER) cc_final: 0.2082 (mmm) REVERT: G 700 ARG cc_start: 0.6247 (ptt180) cc_final: 0.5949 (ptt-90) REVERT: G 924 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7300 (mt) REVERT: I 184 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: I 259 THR cc_start: 0.8468 (p) cc_final: 0.8220 (p) REVERT: J 84 MET cc_start: 0.8567 (ttp) cc_final: 0.8324 (ttp) REVERT: J 184 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4971 (m-10) REVERT: J 240 MET cc_start: 0.8307 (tmt) cc_final: 0.7923 (tmt) REVERT: J 289 THR cc_start: 0.8974 (m) cc_final: 0.8642 (t) REVERT: J 292 TYR cc_start: 0.8470 (m-80) cc_final: 0.8171 (m-80) REVERT: J 734 SER cc_start: 0.7068 (m) cc_final: 0.6527 (t) REVERT: J 862 ILE cc_start: 0.0197 (OUTLIER) cc_final: -0.0705 (mp) REVERT: J 1108 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8706 (mttt) REVERT: K 159 ASN cc_start: 0.6833 (p0) cc_final: 0.5647 (m110) outliers start: 79 outliers final: 51 residues processed: 361 average time/residue: 1.1365 time to fit residues: 523.1983 Evaluate side-chains 339 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 277 ASN Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 563 MET Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 924 ILE Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1108 LYS Chi-restraints excluded: chain J residue 1139 VAL Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 303 optimal weight: 1.9990 chunk 406 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 382 optimal weight: 7.9990 chunk 159 optimal weight: 0.4980 chunk 392 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 808 GLN G 999 ASN G1009 GLN G1023 GLN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1146 HIS ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS I 766 HIS I 819 GLN I 974 GLN I1145 ASN ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN J 765 ASN ** J 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1208 GLN ** J1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.130199 restraints weight = 159563.762| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 5.43 r_work: 0.3867 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 1.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 37966 Z= 0.365 Angle : 0.823 16.700 51670 Z= 0.426 Chirality : 0.051 0.569 5813 Planarity : 0.006 0.094 6698 Dihedral : 6.048 59.789 5259 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.17 % Favored : 90.58 % Rotamer: Outliers : 2.49 % Allowed : 30.60 % Favored : 66.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4813 helix: 0.22 (0.19), residues: 755 sheet: -0.82 (0.15), residues: 1251 loop : -1.92 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 47 HIS 0.016 0.002 HIS G 167 PHE 0.056 0.003 PHE J 788 TYR 0.044 0.002 TYR G 314 ARG 0.014 0.001 ARG A 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14207.22 seconds wall clock time: 252 minutes 51.17 seconds (15171.17 seconds total)