Starting phenix.real_space_refine on Tue Apr 16 05:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/04_2024/7x28_32961_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/04_2024/7x28_32961.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/7x28_32961/04_2024/7x28_32961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/04_2024/7x28_32961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/04_2024/7x28_32961_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/04_2024/7x28_32961_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 5870 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 155 5.16 5 C 20027 2.51 5 N 5245 2.21 5 O 6156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 505": "NH1" <-> "NH2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F GLU 823": "OE1" <-> "OE2" Residue "F ASP 940": "OD1" <-> "OD2" Residue "F GLU 1039": "OE1" <-> "OE2" Residue "F GLU 1062": "OE1" <-> "OE2" Residue "F ARG 1074": "NH1" <-> "NH2" Residue "F GLU 1090": "OE1" <-> "OE2" Residue "F GLU 1148": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 505": "NH1" <-> "NH2" Residue "G GLU 589": "OE1" <-> "OE2" Residue "G PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1039": "OE1" <-> "OE2" Residue "G GLU 1090": "OE1" <-> "OE2" Residue "G GLU 1148": "OE1" <-> "OE2" Residue "G TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 247": "OE1" <-> "OE2" Residue "I ARG 301": "NH1" <-> "NH2" Residue "I GLU 357": "OE1" <-> "OE2" Residue "I GLU 605": "OE1" <-> "OE2" Residue "I TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1039": "OE1" <-> "OE2" Residue "I GLU 1090": "OE1" <-> "OE2" Residue "I GLU 1148": "OE1" <-> "OE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" 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-5288/modules/chem_data/mon_lib" Total number of atoms: 31583 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" 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: "D" 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: "F" Number of atoms: 8947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8947 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 58, 'TRANS': 1098} Chain breaks: 4 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: "G" Number of atoms: 8852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8852 Classifications: {'peptide': 1147} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 58, 'TRANS': 1086} Chain breaks: 5 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: 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: "I" Number of atoms: 7316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7316 Classifications: {'peptide': 947} Link IDs: {'PTRANS': 44, 'TRANS': 902} Chain breaks: 5 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: 16.11, per 1000 atoms: 0.51 Number of scatterers: 31583 At special positions: 0 Unit cell: (149.385, 200.262, 239.232, 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 155 16.00 O 6156 8.00 N 5245 7.00 C 20027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 383 " - pdb=" SG CYS F 407 " distance=2.04 Simple disulfide: pdb=" SG CYS F 425 " - pdb=" SG CYS F 478 " distance=2.04 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.04 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.03 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.04 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.03 Simple disulfide: pdb=" SG CYS F 806 " - pdb=" SG CYS F 828 " distance=2.04 Simple disulfide: pdb=" SG CYS F 811 " - pdb=" SG CYS F 817 " distance=2.03 Simple disulfide: pdb=" SG CYS F 912 " - pdb=" SG CYS F 925 " distance=2.03 Simple disulfide: pdb=" SG CYS F1106 " - pdb=" SG CYS F1117 " distance=2.03 Simple disulfide: pdb=" SG CYS F1156 " - pdb=" SG CYS F1164 " 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS G 425 " - pdb=" SG CYS G 478 " distance=2.04 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 585 " distance=2.03 Simple disulfide: pdb=" SG CYS G 503 " - pdb=" SG CYS G 526 " distance=2.04 Simple disulfide: pdb=" SG CYS G 603 " - pdb=" SG CYS G 654 " distance=2.04 Simple disulfide: pdb=" SG CYS G 620 " - pdb=" SG CYS G 650 " distance=2.03 Simple disulfide: pdb=" SG CYS G 679 " - pdb=" SG CYS G 713 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.02 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 603 " - pdb=" SG CYS I 654 " distance=2.03 Simple disulfide: pdb=" SG CYS I 620 " - pdb=" SG CYS I 650 " distance=2.03 Simple disulfide: pdb=" SG CYS I 679 " - pdb=" SG CYS I 713 " distance=2.04 Simple disulfide: pdb=" SG CYS I 727 " - pdb=" SG CYS I 736 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.04 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 K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.31 Conformation dependent library (CDL) restraints added in 7.2 seconds 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7620 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 71 sheets defined 21.3% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 268 through 273 removed outlier: 3.752A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 Processing helix chain 'F' and resid 410 through 418 removed outlier: 3.737A pdb=" N LEU F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 524 through 528 removed outlier: 4.413A pdb=" N SER F 528 " --> pdb=" O PRO F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 682 Processing helix chain 'F' and resid 805 through 811 Processing helix chain 'F' and resid 815 through 824 Processing helix chain 'F' and resid 825 through 854 Processing helix chain 'F' and resid 888 through 898 Processing helix chain 'F' and resid 907 through 916 removed outlier: 3.735A pdb=" N GLN F 914 " --> pdb=" O ASP F 910 " (cutoff:3.500A) Processing helix chain 'F' and resid 922 through 931 Processing helix chain 'F' and resid 940 through 959 removed outlier: 3.560A pdb=" N ALA F 956 " --> pdb=" O LEU F 952 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY F 957 " --> pdb=" O GLY F 953 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY F 959 " --> pdb=" O ILE F 955 " (cutoff:3.500A) Processing helix chain 'F' and resid 971 through 984 Processing helix chain 'F' and resid 986 through 993 Processing helix chain 'F' and resid 993 through 1010 Processing helix chain 'F' and resid 1016 through 1042 Processing helix chain 'F' and resid 1051 through 1057 removed outlier: 3.804A pdb=" N ILE F1055 " --> pdb=" O ILE F1051 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN F1056 " --> pdb=" O GLY F1052 " (cutoff:3.500A) Processing helix chain 'F' and resid 1059 through 1066 removed outlier: 3.521A pdb=" N GLN F1063 " --> pdb=" O ASP F1059 " (cutoff:3.500A) Processing helix chain 'F' and resid 1067 through 1106 Processing helix chain 'F' and resid 1198 through 1200 No H-bonds generated for 'chain 'F' and resid 1198 through 1200' Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 209 through 214 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 268 through 273 removed outlier: 4.190A pdb=" N LEU G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 352 Processing helix chain 'G' and resid 385 through 390 Processing helix chain 'G' and resid 410 through 418 removed outlier: 3.665A pdb=" N LEU G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 435 Processing helix chain 'G' and resid 449 through 453 removed outlier: 3.567A pdb=" N MET G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 468 Processing helix chain 'G' and resid 678 through 682 Processing helix chain 'G' and resid 805 through 811 Processing helix chain 'G' and resid 814 through 825 Processing helix chain 'G' and resid 826 through 854 Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 916 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.529A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 959 removed outlier: 3.768A pdb=" N ALA G 956 " --> pdb=" O LEU G 952 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY G 957 " --> pdb=" O GLY G 953 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY G 959 " --> pdb=" O ILE G 955 " (cutoff:3.500A) Processing helix chain 'G' and resid 971 through 983 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1010 Processing helix chain 'G' and resid 1016 through 1041 removed outlier: 3.512A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER G1041 " --> pdb=" O ALA G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1106 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 342 through 352 Processing helix chain 'I' and resid 608 through 611 Processing helix chain 'I' and resid 805 through 810 Processing helix chain 'I' and resid 814 through 825 Processing helix chain 'I' and resid 826 through 854 Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 916 Processing helix chain 'I' and resid 922 through 931 removed outlier: 3.517A pdb=" N TYR I 928 " --> pdb=" O ILE I 924 " (cutoff:3.500A) Processing helix chain 'I' and resid 940 through 959 removed outlier: 3.875A pdb=" N ALA I 956 " --> pdb=" O LEU I 952 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY I 957 " --> pdb=" O GLY I 953 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY I 959 " --> pdb=" O ILE I 955 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 984 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1010 Processing helix chain 'I' and resid 1016 through 1042 removed outlier: 3.547A pdb=" N SER I1041 " --> pdb=" O ALA I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1058 Processing helix chain 'I' and resid 1059 through 1106 Processing helix chain 'I' and resid 1219 through 1223 Processing helix chain 'K' and resid 122 through 128 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.812A pdb=" N VAL C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.538A pdb=" N THR C 117 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 160 removed outlier: 4.482A pdb=" N CYS C 203 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 216 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 212 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.621A pdb=" N SER D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.536A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 154 through 155 removed outlier: 3.601A pdb=" N LYS D 146 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 33 through 34 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 64 removed outlier: 6.787A pdb=" N THR F 63 " --> pdb=" O TYR I 632 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL I 631 " --> pdb=" O VAL I 639 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 617 " --> pdb=" O ASN I 602 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN I 602 " --> pdb=" O PHE I 617 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 75 removed outlier: 4.214A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 83 through 86 removed outlier: 5.753A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.051A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR F 206 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AB8, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.487A pdb=" N ALA F 146 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER F 151 " --> pdb=" O HIS F 167 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N HIS F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL F 153 " --> pdb=" O PHE F 165 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE F 165 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N PHE F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN F 166 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU F 187 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU F 180 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 241 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA F 182 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE F 239 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR F 184 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N CYS F 237 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 129 Processing sheet with id=AC1, first strand: chain 'F' and resid 359 through 366 removed outlier: 4.578A pdb=" N VAL F 659 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER F 365 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL F 657 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR F 669 " --> pdb=" O ASP F 664 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 373 through 374 removed outlier: 6.937A pdb=" N VAL F 374 " --> pdb=" O SER F 607 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 400 through 404 removed outlier: 6.339A pdb=" N THR F 483 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL F 420 " --> pdb=" O THR F 483 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 513 through 515 removed outlier: 3.712A pdb=" N TYR F 497 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER F 557 " --> pdb=" O ASN F 501 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N CYS F 503 " --> pdb=" O VAL F 555 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL F 555 " --> pdb=" O CYS F 503 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG F 505 " --> pdb=" O TRP F 553 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP F 553 " --> pdb=" O ARG F 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 707 through 708 Processing sheet with id=AC6, first strand: chain 'F' and resid 718 through 724 removed outlier: 9.075A pdb=" N VAL F 718 " --> pdb=" O GLY F 755 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET F 757 " --> pdb=" O VAL F 718 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER F 720 " --> pdb=" O MET F 757 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU F 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU F 722 " --> pdb=" O LEU F 759 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 761 " --> pdb=" O LEU F 722 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU F 756 " --> pdb=" O ASP F 740 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP F 740 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY F 732 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALA F 737 " --> pdb=" O PRO F 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 768 through 769 removed outlier: 5.484A pdb=" N ILE F 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 1121 through 1128 removed outlier: 5.674A pdb=" N HIS F1122 " --> pdb=" O TYR F1141 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR F1141 " --> pdb=" O HIS F1122 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE F1172 " --> pdb=" O ALA F1152 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F1188 " --> pdb=" O ALA F1193 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA F1193 " --> pdb=" O GLY F1188 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 1121 through 1128 removed outlier: 5.674A pdb=" N HIS F1122 " --> pdb=" O TYR F1141 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR F1141 " --> pdb=" O HIS F1122 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS F1146 " --> pdb=" O PRO F 783 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU F1148 " --> pdb=" O SER F 781 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER F 781 " --> pdb=" O GLU F1148 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F1150 " --> pdb=" O LYS F 779 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS F 779 " --> pdb=" O VAL F1150 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 801 through 803 removed outlier: 4.363A pdb=" N LYS F 801 " --> pdb=" O LEU F 935 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 857 through 858 Processing sheet with id=AD3, first strand: chain 'F' and resid 967 through 968 removed outlier: 6.737A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR I1135 " --> pdb=" O VAL I1127 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL I1127 " --> pdb=" O TYR I1135 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET I1137 " --> pdb=" O SER I1125 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER I1125 " --> pdb=" O MET I1137 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL I1139 " --> pdb=" O ILE I1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 967 through 968 removed outlier: 6.737A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 1202 through 1204 Processing sheet with id=AD6, first strand: chain 'G' and resid 33 through 34 Processing sheet with id=AD7, first strand: chain 'G' and resid 68 through 75 removed outlier: 3.533A pdb=" N ILE G 69 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY G 115 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER G 267 " --> pdb=" O GLN G 280 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN G 280 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 83 through 86 removed outlier: 4.087A pdb=" N ARG G 335 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 88 through 89 removed outlier: 7.090A pdb=" N SER G 88 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR G 206 " --> pdb=" O SER G 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain 'G' and resid 110 through 111 removed outlier: 4.516A pdb=" N ALA G 146 " --> pdb=" O ILE G 296 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR G 184 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE G 239 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE G 186 " --> pdb=" O CYS G 237 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N CYS G 237 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU G 188 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG G 235 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 127 through 129 Processing sheet with id=AE4, first strand: chain 'G' and resid 359 through 366 removed outlier: 4.562A pdb=" N VAL G 659 " --> pdb=" O VAL G 363 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER G 365 " --> pdb=" O VAL G 657 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL G 657 " --> pdb=" O SER G 365 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR G 669 " --> pdb=" O ASP G 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 373 through 374 removed outlier: 7.004A pdb=" N VAL G 374 " --> pdb=" O SER G 607 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL G 639 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE G 630 " --> pdb=" O THR I 63 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 400 through 404 removed outlier: 6.353A pdb=" N THR G 483 " --> pdb=" O VAL G 420 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL G 420 " --> pdb=" O THR G 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 408 through 409 Processing sheet with id=AE8, first strand: chain 'G' and resid 513 through 515 removed outlier: 5.743A pdb=" N SER G 498 " --> pdb=" O VAL G 561 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL G 561 " --> pdb=" O SER G 498 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE G 500 " --> pdb=" O SER G 559 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER G 559 " --> pdb=" O ILE G 500 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS G 502 " --> pdb=" O SER G 557 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP G 553 " --> pdb=" O LEU G 506 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 718 through 724 removed outlier: 7.077A pdb=" N VAL G 718 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N SER G 761 " --> pdb=" O VAL G 718 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N SER G 720 " --> pdb=" O SER G 761 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU G 756 " --> pdb=" O ASP G 740 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP G 740 " --> pdb=" O GLU G 756 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY G 732 " --> pdb=" O LEU G 735 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA G 737 " --> pdb=" O PRO G 730 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 768 through 769 removed outlier: 5.492A pdb=" N ILE G 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 5.864A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY G1188 " --> pdb=" O ALA G1193 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA G1193 " --> pdb=" O GLY G1188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 5.864A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 801 through 803 removed outlier: 4.308A pdb=" N LYS G 801 " --> pdb=" O LEU G 935 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1202 through 1204 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.701A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.039A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 127 through 128 removed outlier: 4.118A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AG1, first strand: chain 'H' and resid 158 through 160 Processing sheet with id=AG2, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AG3, first strand: chain 'I' and resid 68 through 75 removed outlier: 4.396A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 83 through 85 removed outlier: 5.955A pdb=" N SER I 267 " --> pdb=" O GLN I 280 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN I 280 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 88 through 89 removed outlier: 3.943A pdb=" N SER I 88 " --> pdb=" O HIS I 298 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE I 300 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'I' and resid 92 through 93 Processing sheet with id=AG7, first strand: chain 'I' and resid 110 through 111 removed outlier: 4.579A pdb=" N SER I 151 " --> pdb=" O HIS I 167 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N HIS I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL I 153 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE I 165 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N PHE I 164 " --> pdb=" O PRO I 189 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN I 166 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU I 187 " --> pdb=" O ASN I 166 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU I 180 " --> pdb=" O TYR I 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR I 241 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA I 182 " --> pdb=" O PHE I 239 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE I 239 " --> pdb=" O ALA I 182 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR I 184 " --> pdb=" O CYS I 237 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS I 237 " --> pdb=" O TYR I 184 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 127 through 129 Processing sheet with id=AG9, first strand: chain 'I' and resid 659 through 664 removed outlier: 3.879A pdb=" N THR I 669 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 707 through 709 Processing sheet with id=AH2, first strand: chain 'I' and resid 718 through 724 removed outlier: 7.536A pdb=" N SER I 761 " --> pdb=" O SER I 720 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU I 722 " --> pdb=" O SER I 761 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU I 756 " --> pdb=" O ASP I 740 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP I 740 " --> pdb=" O GLU I 756 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 729 " --> pdb=" O ALA I 737 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 801 through 803 removed outlier: 4.483A pdb=" N LYS I 801 " --> pdb=" O LEU I 935 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 1202 through 1204 Processing sheet with id=AH5, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.569A pdb=" N LEU K 11 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU K 106 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.879A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 115 through 119 removed outlier: 3.539A pdb=" N VAL K 134 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 154 through 155 removed outlier: 3.731A pdb=" N LYS K 146 " --> pdb=" O THR K 198 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3373 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: 19.25 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5348 1.32 - 1.44: 8881 1.44 - 1.57: 17879 1.57 - 1.69: 9 1.69 - 1.81: 200 Bond restraints: 32317 Sorted by residual: bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.235 1.366 -0.131 1.14e-02 7.69e+03 1.32e+02 bond pdb=" C SER C 160 " pdb=" O SER C 160 " ideal model delta sigma weight residual 1.236 1.365 -0.129 1.20e-02 6.94e+03 1.16e+02 bond pdb=" C SER C 186 " pdb=" O SER C 186 " ideal model delta sigma weight residual 1.236 1.363 -0.128 1.20e-02 6.94e+03 1.14e+02 bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.364 -0.128 1.21e-02 6.83e+03 1.12e+02 bond pdb=" N CYS F 585 " pdb=" CA CYS F 585 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.92e+01 ... (remaining 32312 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.79: 1028 106.79 - 113.72: 17286 113.72 - 120.65: 15081 120.65 - 127.58: 10439 127.58 - 134.51: 148 Bond angle restraints: 43982 Sorted by residual: angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.34 -11.96 1.09e+00 8.42e-01 1.20e+02 angle pdb=" O SER C 186 " pdb=" C SER C 186 " pdb=" CA ASER C 186 " ideal model delta sigma weight residual 120.36 132.15 -11.79 1.08e+00 8.57e-01 1.19e+02 angle pdb=" O SER C 186 " pdb=" C SER C 186 " pdb=" CA BSER C 186 " ideal model delta sigma weight residual 120.36 132.15 -11.79 1.08e+00 8.57e-01 1.19e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.25 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" O SER C 160 " pdb=" C SER C 160 " pdb=" CA BSER C 160 " ideal model delta sigma weight residual 120.36 131.97 -11.61 1.08e+00 8.57e-01 1.16e+02 ... (remaining 43977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17659 17.86 - 35.72: 1234 35.72 - 53.58: 308 53.58 - 71.44: 80 71.44 - 89.31: 12 Dihedral angle restraints: 19293 sinusoidal: 7344 harmonic: 11949 Sorted by residual: dihedral pdb=" CB CYS F 811 " pdb=" SG CYS F 811 " pdb=" SG CYS F 817 " pdb=" CB CYS F 817 " ideal model delta sinusoidal sigma weight residual -86.00 -165.04 79.04 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CA LEU G 548 " pdb=" C LEU G 548 " pdb=" N GLU G 549 " pdb=" CA GLU G 549 " ideal model delta harmonic sigma weight residual 0.00 33.07 -33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CB CYS F 806 " pdb=" SG CYS F 806 " pdb=" SG CYS F 828 " pdb=" CB CYS F 828 " ideal model delta sinusoidal sigma weight residual 93.00 45.76 47.24 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 19290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3901 0.140 - 0.279: 1010 0.279 - 0.419: 17 0.419 - 0.559: 4 0.559 - 0.698: 2 Chirality restraints: 4934 Sorted by residual: chirality pdb=" CG LEU F1222 " pdb=" CB LEU F1222 " pdb=" CD1 LEU F1222 " pdb=" CD2 LEU F1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CG LEU G1222 " pdb=" CB LEU G1222 " pdb=" CD1 LEU G1222 " pdb=" CD2 LEU G1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA BSER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB BSER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 4931 not shown) Planarity restraints: 5708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F1066 " -0.013 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C GLN F1066 " 0.048 2.00e-02 2.50e+03 pdb=" O GLN F1066 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE F1067 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G1192 " 0.032 2.00e-02 2.50e+03 1.73e-02 6.01e+00 pdb=" CG TYR G1192 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR G1192 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR G1192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR G1192 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR G1192 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR G1192 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR G1192 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F1192 " -0.032 2.00e-02 2.50e+03 1.73e-02 5.98e+00 pdb=" CG TYR F1192 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR F1192 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F1192 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F1192 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F1192 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR F1192 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F1192 " -0.026 2.00e-02 2.50e+03 ... (remaining 5705 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 1 2.27 - 2.92: 13044 2.92 - 3.58: 45182 3.58 - 4.24: 78178 4.24 - 4.90: 127790 Nonbonded interactions: 264195 Sorted by model distance: nonbonded pdb=" CB ALA F1130 " pdb=" O GLY F1133 " model vdw 1.606 3.460 nonbonded pdb=" CA ALA G 53 " pdb=" CD1 ILE G 56 " model vdw 2.265 3.890 nonbonded pdb=" CB ALA G 53 " pdb=" CD1 ILE G 56 " model vdw 2.367 3.880 nonbonded pdb=" O SER F 546 " pdb=" O GLU F 549 " model vdw 2.421 3.040 nonbonded pdb=" N GLY I 90 " pdb=" O ILE I 300 " model vdw 2.439 2.520 ... (remaining 264190 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 'C' and (resid 1 through 159 or resid 161 through 185 or resid 187 throug \ h 221)) selection = (chain 'H' and (resid 1 through 159 or resid 161 through 185 or resid 187 throug \ h 221)) } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 18 through 153 or resid 166 through 1224)) selection = chain 'G' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.030 Extract box with map and model: 8.660 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 90.640 Find NCS groups from input model: 2.270 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3881 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 : 0.013 0.141 32317 Z= 0.886 Angle : 1.522 21.819 43982 Z= 1.181 Chirality : 0.109 0.698 4934 Planarity : 0.004 0.035 5708 Dihedral : 13.241 89.306 11508 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.72 % Favored : 97.03 % Rotamer: Outliers : 7.98 % Allowed : 8.27 % Favored : 83.75 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 2.21 (0.13), residues: 4081 helix: 4.14 (0.17), residues: 800 sheet: 1.74 (0.16), residues: 1068 loop : 0.35 (0.12), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F1184 HIS 0.005 0.001 HIS C 207 PHE 0.016 0.002 PHE G 895 TYR 0.032 0.002 TYR F1192 ARG 0.005 0.001 ARG I 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 516 time to evaluate : 3.242 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: D 190 HIS cc_start: -0.2560 (OUTLIER) cc_final: -0.2951 (t-90) REVERT: G 809 TYR cc_start: 0.3194 (t80) cc_final: 0.2729 (t80) REVERT: G 909 TYR cc_start: -0.0661 (OUTLIER) cc_final: -0.1353 (t80) REVERT: K 147 VAL cc_start: -0.0187 (OUTLIER) cc_final: -0.0421 (t) outliers start: 277 outliers final: 44 residues processed: 740 average time/residue: 1.1050 time to fit residues: 1013.1340 Evaluate side-chains 338 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain F residue 71 TYR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 590 PHE Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 831 ILE Chi-restraints excluded: chain F residue 836 HIS Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 422 ASP Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 1015 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 254 PHE Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1015 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 GLN Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 0.9980 chunk 310 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 320 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 0.0050 chunk 371 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 112 GLN C 178 GLN C 199 GLN C 204 ASN F 36 GLN F 166 ASN F 236 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 521 ASN F 582 ASN F 592 ASN F 628 GLN F 733 GLN F 815 GLN F 819 GLN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 981 ASN F1009 GLN F1042 ASN F1063 GLN F1066 GLN F1085 GLN ** F1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1213 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 HIS G 236 ASN G 280 GLN G 521 ASN G 544 GLN G 576 GLN G 599 GLN ** G 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 628 GLN G 681 HIS ** G 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 981 ASN G1072 ASN G1213 ASN H 6 GLN H 162 ASN H 178 GLN I 60 GLN I 166 ASN I 208 HIS ** I 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN I 277 ASN I 280 GLN I 348 HIS I 599 GLN I 628 GLN I 681 HIS ** I 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 766 HIS I 769 GLN ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 981 ASN I1020 GLN ** I1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1072 ASN I1213 ASN I1217 ASN K 43 GLN K 148 GLN K 161 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4291 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 32317 Z= 0.240 Angle : 0.679 18.141 43982 Z= 0.357 Chirality : 0.046 0.295 4934 Planarity : 0.004 0.048 5708 Dihedral : 6.172 59.506 4537 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.79 % Favored : 98.09 % Rotamer: Outliers : 4.52 % Allowed : 16.05 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.13), residues: 4081 helix: 2.60 (0.18), residues: 789 sheet: 1.17 (0.15), residues: 1125 loop : 0.05 (0.12), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 47 HIS 0.019 0.001 HIS G 836 PHE 0.027 0.002 PHE G 827 TYR 0.030 0.002 TYR G 824 ARG 0.008 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 319 time to evaluate : 3.434 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: D 190 HIS cc_start: -0.2425 (OUTLIER) cc_final: -0.2851 (t-90) REVERT: F 757 MET cc_start: 0.2946 (pmm) cc_final: 0.2719 (mpt) REVERT: F 960 TRP cc_start: 0.4862 (OUTLIER) cc_final: 0.4268 (t60) REVERT: G 909 TYR cc_start: -0.0700 (OUTLIER) cc_final: -0.1230 (t80) REVERT: H 50 ARG cc_start: 0.3876 (ttp80) cc_final: 0.2997 (tmm160) REVERT: I 84 MET cc_start: 0.3314 (OUTLIER) cc_final: 0.2923 (tmt) REVERT: I 174 ASP cc_start: -0.0992 (OUTLIER) cc_final: -0.1351 (m-30) REVERT: I 642 TYR cc_start: 0.0007 (m-80) cc_final: -0.0203 (t80) REVERT: I 757 MET cc_start: 0.2295 (OUTLIER) cc_final: 0.1795 (mpt) outliers start: 158 outliers final: 61 residues processed: 443 average time/residue: 1.1323 time to fit residues: 623.6719 Evaluate side-chains 306 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 532 SER Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 590 PHE Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 734 SER Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 960 TRP Chi-restraints excluded: chain F residue 1150 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 416 SER Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 542 ARG Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 836 HIS Chi-restraints excluded: chain G residue 854 LYS Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 254 PHE Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 372 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 368 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 812 ASN F 839 ASN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 277 ASN G 280 GLN G 421 ASN ** G 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 812 ASN G 833 GLN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN ** I 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 733 GLN I 988 GLN I1132 ASN I1217 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 32317 Z= 0.427 Angle : 0.834 16.210 43982 Z= 0.453 Chirality : 0.053 0.226 4934 Planarity : 0.007 0.129 5708 Dihedral : 6.341 59.452 4495 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 5.61 % Allowed : 15.25 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 4081 helix: 0.90 (0.18), residues: 802 sheet: 0.50 (0.15), residues: 1064 loop : -0.39 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP K 36 HIS 0.023 0.003 HIS G 836 PHE 0.052 0.003 PHE I 354 TYR 0.041 0.003 TYR F 270 ARG 0.023 0.002 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 305 time to evaluate : 3.404 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: D 190 HIS cc_start: -0.2256 (OUTLIER) cc_final: -0.2967 (t-90) REVERT: F 240 MET cc_start: 0.3379 (OUTLIER) cc_final: 0.3006 (tmt) REVERT: G 303 ILE cc_start: -0.0063 (OUTLIER) cc_final: -0.0475 (pp) REVERT: G 757 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5516 (mtm) REVERT: G 809 TYR cc_start: 0.5104 (t80) cc_final: 0.4107 (t80) REVERT: G 909 TYR cc_start: 0.1468 (OUTLIER) cc_final: 0.1162 (t80) REVERT: H 145 LEU cc_start: 0.5209 (OUTLIER) cc_final: 0.4959 (pp) REVERT: I 174 ASP cc_start: 0.0828 (OUTLIER) cc_final: 0.0430 (m-30) REVERT: I 927 GLN cc_start: 0.3689 (mt0) cc_final: 0.2883 (mt0) outliers start: 196 outliers final: 65 residues processed: 459 average time/residue: 1.0692 time to fit residues: 605.8567 Evaluate side-chains 300 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 228 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 958 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain F residue 1185 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 243 TYR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 416 SER Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 542 ARG Chi-restraints excluded: chain G residue 571 PHE Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 717 LEU Chi-restraints excluded: chain G residue 757 MET Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 836 HIS Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 943 MET Chi-restraints excluded: chain I residue 995 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 190 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 249 optimal weight: 0.5980 chunk 373 optimal weight: 0.9980 chunk 395 optimal weight: 50.0000 chunk 195 optimal weight: 8.9990 chunk 353 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: