Starting phenix.real_space_refine on Sat Mar 23 15:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/03_2024/7x28_32961_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/03_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_32961/03_2024/7x28_32961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/03_2024/7x28_32961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/03_2024/7x28_32961_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x28_32961/03_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 17.40, per 1000 atoms: 0.55 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: 10.89 Conformation dependent library (CDL) restraints added in 6.7 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: 4.61 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: 16.22 Time building geometry restraints manager: 12.09 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 8.570 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 86.660 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.160 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.400 ------------------------------------------------------------------------------- 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 : 3.721 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: 1.0357 time to fit residues: 949.9960 Evaluate side-chains 338 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 3.439 ------------------------------------------------------------------------------- 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 : 3.597 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: 1.0803 time to fit residues: 596.6808 Evaluate side-chains 306 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 3.607 ------------------------------------------------------------------------------- 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 : 3.470 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: 1.0935 time to fit residues: 621.4285 Evaluate side-chains 300 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 228 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 65 GLN F 78 GLN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 733 GLN F 800 GLN ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 914 GLN ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN ** G 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 GLN G 833 GLN ** I 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 GLN ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32317 Z= 0.345 Angle : 0.745 16.238 43982 Z= 0.390 Chirality : 0.048 0.275 4934 Planarity : 0.005 0.072 5708 Dihedral : 5.683 59.404 4482 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.89 % Favored : 96.96 % Rotamer: Outliers : 4.20 % Allowed : 17.76 % Favored : 78.03 % 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: 1.22 (0.18), residues: 797 sheet: 0.47 (0.16), residues: 1002 loop : -0.48 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 47 HIS 0.025 0.002 HIS F 81 PHE 0.025 0.003 PHE F 281 TYR 0.027 0.002 TYR F 932 ARG 0.014 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 4 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 427 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 280 time to evaluate : 3.606 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: D 82 GLU cc_start: 0.1718 (OUTLIER) cc_final: 0.1494 (pt0) REVERT: D 190 HIS cc_start: -0.2200 (OUTLIER) cc_final: -0.2827 (t-90) REVERT: F 232 PHE cc_start: 0.0817 (OUTLIER) cc_final: 0.0600 (m-10) REVERT: F 757 MET cc_start: 0.4122 (mpt) cc_final: 0.3905 (mpt) REVERT: G 232 PHE cc_start: 0.2240 (OUTLIER) cc_final: 0.2019 (m-10) REVERT: H 145 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.5001 (pp) REVERT: I 174 ASP cc_start: 0.0834 (OUTLIER) cc_final: 0.0298 (m-30) outliers start: 147 outliers final: 60 residues processed: 402 average time/residue: 1.0341 time to fit residues: 523.5314 Evaluate side-chains 307 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 241 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL 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 185 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 179 THR 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 232 PHE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 513 GLU 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 635 TYR Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 909 TYR Chi-restraints excluded: chain F residue 1071 ILE Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 758 ARG Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 836 HIS Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 964 LEU Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1043 THR Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 1063 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 294 optimal weight: 0.0570 chunk 163 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 273 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 354 optimal weight: 1.9990 chunk 99 optimal weight: 0.0670 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 HIS F 277 ASN F 636 GLN ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 988 GLN F1132 ASN ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 GLN G 826 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 HIS ** I 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 927 GLN I 988 GLN I1079 ASN I1110 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32317 Z= 0.181 Angle : 0.629 15.910 43982 Z= 0.324 Chirality : 0.044 0.257 4934 Planarity : 0.004 0.052 5708 Dihedral : 5.227 59.012 4477 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 3.52 % Allowed : 19.08 % Favored : 77.40 % 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: 0.25 (0.13), residues: 4081 helix: 1.49 (0.18), residues: 803 sheet: 0.55 (0.16), residues: 973 loop : -0.46 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 47 HIS 0.017 0.001 HIS G 836 PHE 0.026 0.002 PHE G 571 TYR 0.026 0.002 TYR F 928 ARG 0.010 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 5 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 375 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 252 time to evaluate : 3.700 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: D 190 HIS cc_start: -0.2175 (OUTLIER) cc_final: -0.2737 (t-90) REVERT: F 469 TYR cc_start: 0.3727 (t80) cc_final: 0.3496 (t80) REVERT: F 757 MET cc_start: 0.4603 (mpt) cc_final: 0.4381 (mpt) REVERT: G 758 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6815 (ttp-110) REVERT: I 174 ASP cc_start: 0.0454 (OUTLIER) cc_final: 0.0245 (m-30) outliers start: 123 outliers final: 61 residues processed: 359 average time/residue: 1.1007 time to fit residues: 493.3251 Evaluate side-chains 292 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 228 time to evaluate : 3.173 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 185 LEU 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 103 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 330 ASP Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 642 TYR Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 758 ARG Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 836 HIS Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1070 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 102 VAL 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 356 VAL Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain K residue 7 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 395 optimal weight: 7.9990 chunk 328 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN F 815 GLN ** F1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 GLN G 544 GLN ** G 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 GLN G 826 GLN G 927 GLN G1063 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 ASN I 348 HIS I 377 GLN I 836 HIS I1110 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.8507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 32317 Z= 0.448 Angle : 0.844 14.970 43982 Z= 0.454 Chirality : 0.054 0.496 4934 Planarity : 0.006 0.117 5708 Dihedral : 6.019 58.914 4475 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 4.46 % Allowed : 18.22 % Favored : 77.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.31 (0.12), residues: 4081 helix: 0.80 (0.18), residues: 789 sheet: 0.24 (0.16), residues: 1015 loop : -0.76 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP C 47 HIS 0.036 0.004 HIS C 171 PHE 0.039 0.003 PHE F 254 TYR 0.055 0.003 TYR I 314 ARG 0.015 0.001 ARG I1057 *********************** REFINEMENT MACRO_CYCLE 6 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 450 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 294 time to evaluate : 3.405 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: -0.2065 (OUTLIER) cc_final: -0.2705 (t-90) REVERT: G 232 PHE cc_start: 0.3002 (OUTLIER) cc_final: 0.2703 (m-10) REVERT: I 1008 MET cc_start: 0.6555 (tmm) cc_final: 0.6314 (ttp) REVERT: K 7 SER cc_start: -0.3239 (OUTLIER) cc_final: -0.3513 (p) outliers start: 156 outliers final: 70 residues processed: 416 average time/residue: 1.1110 time to fit residues: 571.8464 Evaluate side-chains 317 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 244 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE 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 148 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 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 103 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 SER 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 117 VAL Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 521 ASN Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 330 ASP Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 810 VAL Chi-restraints excluded: chain G residue 821 LEU Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 964 LEU Chi-restraints excluded: chain G residue 986 THR Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 261 GLN Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 664 ASP Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain K residue 78 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 288 optimal weight: 50.0000 chunk 223 optimal weight: 0.6980 chunk 333 optimal weight: 0.0870 chunk 220 optimal weight: 3.9990 chunk 394 optimal weight: 30.0000 chunk 246 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** F 72 GLN ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN G 280 GLN G 826 GLN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1063 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 HIS I 377 GLN I 915 GLN I1063 GLN I1110 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 moved from start: 0.8725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.201 32317 Z= 0.232 Angle : 0.682 14.139 43982 Z= 0.353 Chirality : 0.045 0.263 4934 Planarity : 0.005 0.058 5708 Dihedral : 5.394 55.455 4474 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.37 % Rotamer: Outliers : 3.09 % Allowed : 20.48 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.07 (0.13), residues: 4081 helix: 1.35 (0.18), residues: 784 sheet: 0.31 (0.16), residues: 965 loop : -0.68 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP C 47 HIS 0.015 0.001 HIS I 670 PHE 0.020 0.002 PHE F 116 TYR 0.047 0.002 TYR I 351 ARG 0.010 0.001 ARG G 401 *********************** REFINEMENT MACRO_CYCLE 7 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 371 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 263 time to evaluate : 3.456 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: F 680 GLU cc_start: 0.3870 (OUTLIER) cc_final: 0.3353 (mt-10) REVERT: G 110 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6327 (mmtm) REVERT: G 232 PHE cc_start: 0.2990 (OUTLIER) cc_final: 0.2529 (m-10) REVERT: G 542 ARG cc_start: 0.3937 (OUTLIER) cc_final: 0.3624 (pmt170) REVERT: G 912 CYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3812 (t) outliers start: 108 outliers final: 60 residues processed: 356 average time/residue: 1.1114 time to fit residues: 492.2538 Evaluate side-chains 286 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 221 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 185 LEU 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 103 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 496 LYS Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 680 GLU Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 1067 ILE Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 110 LYS Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 330 ASP Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 542 ARG Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 361 TYR Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 844 ASP Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 78 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 268 optimal weight: 0.5980 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 309 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** F 72 GLN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN ** G 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 GLN G 836 HIS ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN I 377 GLN I1110 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.9348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 32317 Z= 0.378 Angle : 0.749 21.256 43982 Z= 0.392 Chirality : 0.048 0.454 4934 Planarity : 0.005 0.052 5708 Dihedral : 5.560 58.611 4474 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.24 % Rotamer: Outliers : 3.55 % Allowed : 20.74 % Favored : 75.72 % 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: -0.25 (0.13), residues: 4081 helix: 1.15 (0.18), residues: 782 sheet: 0.14 (0.16), residues: 1003 loop : -0.76 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP C 47 HIS 0.017 0.002 HIS I 670 PHE 0.054 0.002 PHE G 399 TYR 0.026 0.002 TYR F 219 ARG 0.011 0.001 ARG I 269 *********************** REFINEMENT MACRO_CYCLE 8 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 372 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 248 time to evaluate : 3.597 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: F 63 THR cc_start: 0.1081 (OUTLIER) cc_final: -0.0101 (p) REVERT: F 84 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6721 (ttt) REVERT: F 680 GLU cc_start: 0.4576 (OUTLIER) cc_final: 0.3381 (mm-30) REVERT: G 140 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.6134 (mm) REVERT: G 167 HIS cc_start: 0.1643 (OUTLIER) cc_final: 0.1145 (t-90) REVERT: G 232 PHE cc_start: 0.3494 (OUTLIER) cc_final: 0.3211 (m-10) REVERT: G 542 ARG cc_start: 0.3835 (OUTLIER) cc_final: 0.3211 (pmt170) REVERT: G 1105 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: I 1008 MET cc_start: 0.6542 (tmm) cc_final: 0.6163 (ttp) outliers start: 124 outliers final: 68 residues processed: 347 average time/residue: 1.0999 time to fit residues: 476.4930 Evaluate side-chains 297 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 221 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 64 PHE 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 148 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 61 ASP 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 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 680 GLU Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 220 ASN Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 478 CYS Chi-restraints excluded: chain G residue 542 ARG Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 900 ILE Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 964 LEU Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1105 GLU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 361 TYR Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 995 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 33 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 8.9990 chunk 377 optimal weight: 0.5980 chunk 344 optimal weight: 0.6980 chunk 367 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 288 optimal weight: 40.0000 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 5.9990 chunk 347 optimal weight: 0.7980 chunk 366 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** F 72 GLN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN G 681 HIS G 826 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 HIS ** I 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN I1110 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.9506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 32317 Z= 0.208 Angle : 0.701 22.015 43982 Z= 0.356 Chirality : 0.045 0.347 4934 Planarity : 0.005 0.144 5708 Dihedral : 5.329 57.893 4474 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.22 % Rotamer: Outliers : 2.40 % Allowed : 22.05 % Favored : 75.54 % 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: -0.14 (0.13), residues: 4081 helix: 1.38 (0.19), residues: 771 sheet: 0.17 (0.16), residues: 1034 loop : -0.72 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP C 47 HIS 0.010 0.001 HIS F 91 PHE 0.047 0.002 PHE G 674 TYR 0.083 0.002 TYR K 33 ARG 0.009 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 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 313 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 229 time to evaluate : 3.568 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: F 84 MET cc_start: 0.7161 (ttt) cc_final: 0.6886 (ttt) REVERT: F 680 GLU cc_start: 0.4803 (OUTLIER) cc_final: 0.4045 (mm-30) REVERT: G 167 HIS cc_start: 0.2107 (OUTLIER) cc_final: 0.1366 (t-90) outliers start: 84 outliers final: 60 residues processed: 300 average time/residue: 1.0683 time to fit residues: 399.6201 Evaluate side-chains 272 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 58 SER 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 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 61 ASP 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 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 425 CYS Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 526 CYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 680 GLU Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 964 LEU Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain K residue 28 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 237 optimal weight: 0.0010 chunk 184 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 407 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 overall best weight: 1.3192 ------------------------------------------------------------------------------- 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 112 GLN F 72 GLN ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS G 261 GLN ** G 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN I1110 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.9838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 32317 Z= 0.266 Angle : 0.705 20.645 43982 Z= 0.360 Chirality : 0.045 0.292 4934 Planarity : 0.006 0.227 5708 Dihedral : 5.340 59.933 4473 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Rotamer: Outliers : 2.23 % Allowed : 22.28 % Favored : 75.49 % 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: -0.15 (0.13), residues: 4081 helix: 1.31 (0.19), residues: 777 sheet: 0.17 (0.16), residues: 1026 loop : -0.71 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP C 47 HIS 0.008 0.001 HIS F 91 PHE 0.031 0.002 PHE C 153 TYR 0.035 0.002 TYR G 287 ARG 0.009 0.001 ARG F 119 ********************** REFINEMENT MACRO_CYCLE 10 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 301 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 3.460 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: F 84 MET cc_start: 0.7282 (ttt) cc_final: 0.6966 (ttt) REVERT: F 446 PHE cc_start: 0.5826 (p90) cc_final: 0.5120 (p90) REVERT: F 680 GLU cc_start: 0.4670 (OUTLIER) cc_final: 0.3954 (mm-30) REVERT: G 84 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7203 (ttt) REVERT: G 167 HIS cc_start: 0.2624 (OUTLIER) cc_final: 0.1841 (t-90) REVERT: G 542 ARG cc_start: 0.3890 (OUTLIER) cc_final: 0.3221 (pmt-80) REVERT: I 854 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7413 (ttmm) outliers start: 78 outliers final: 59 residues processed: 289 average time/residue: 1.0772 time to fit residues: 392.0758 Evaluate side-chains 276 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 212 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 58 SER 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 148 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain D residue 61 ASP 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 183 SER Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain F residue 451 SER Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 635 TYR Chi-restraints excluded: chain F residue 680 GLU Chi-restraints excluded: chain F residue 810 VAL Chi-restraints excluded: chain F residue 900 ILE Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain G residue 542 ARG Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 827 PHE Chi-restraints excluded: chain G residue 912 CYS Chi-restraints excluded: chain G residue 964 LEU Chi-restraints excluded: chain G residue 988 GLN Chi-restraints excluded: chain G residue 1059 ASP Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 673 LEU Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 736 CYS Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain K residue 33 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 299 optimal weight: 0.5980 chunk 47 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 324 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 333 optimal weight: 0.6980 chunk 41 optimal weight: 50.0000 chunk 59 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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** F 72 GLN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** F 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN I 377 GLN I 808 GLN I1110 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.170931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.132233 restraints weight = 126002.022| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 5.32 r_work: 0.3533 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.9929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 32317 Z= 0.199 Angle : 0.686 19.015 43982 Z= 0.347 Chirality : 0.044 0.333 4934 Planarity : 0.005 0.102 5708 Dihedral : 5.174 59.888 4473 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.05 % Rotamer: Outliers : 1.97 % Allowed : 22.83 % Favored : 75.20 % 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: -0.10 (0.13), residues: 4081 helix: 1.48 (0.19), residues: 771 sheet: 0.19 (0.16), residues: 1026 loop : -0.71 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP C 47 HIS 0.006 0.001 HIS I 298 PHE 0.026 0.002 PHE G 674 TYR 0.028 0.002 TYR F 219 ARG 0.015 0.001 ARG I 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11782.18 seconds wall clock time: 209 minutes 38.82 seconds (12578.82 seconds total)