Starting phenix.real_space_refine on Sat Aug 10 20:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b92_44366/08_2024/9b92_44366.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b92_44366/08_2024/9b92_44366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b92_44366/08_2024/9b92_44366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b92_44366/08_2024/9b92_44366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b92_44366/08_2024/9b92_44366.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b92_44366/08_2024/9b92_44366.cif" } resolution = 3.5 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 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 19404 2.51 5 N 5288 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29948 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7486 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 43, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 275 Chain: "B" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7486 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 43, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 275 Chain: "C" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7486 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 43, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 275 Chain: "D" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7486 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 43, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 275 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.83, per 1000 atoms: 0.53 Number of scatterers: 29948 At special positions: 0 Unit cell: (164.772, 164.772, 161.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 5100 8.00 N 5288 7.00 C 19404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.97 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.97 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.97 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.97 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.33 Conformation dependent library (CDL) restraints added in 5.6 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 68.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.413A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.585A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.675A pdb=" N ILE A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.546A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 removed outlier: 3.838A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 606 through 633 Processing helix chain 'A' and resid 635 through 645 removed outlier: 3.513A pdb=" N ALA A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.853A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 4.106A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.503A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL A 912 " --> pdb=" O ILE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.833A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 3.978A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1143 Processing helix chain 'A' and resid 1143 through 1177 removed outlier: 4.061A pdb=" N ARG A1177 " --> pdb=" O LYS A1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 4.413A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.585A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.674A pdb=" N ILE B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.545A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.838A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 606 through 633 Processing helix chain 'B' and resid 635 through 645 removed outlier: 3.513A pdb=" N ALA B 639 " --> pdb=" O GLU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.853A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 862 removed outlier: 4.107A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 905 removed outlier: 3.502A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL B 912 " --> pdb=" O ILE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.833A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1088 removed outlier: 3.978A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1143 Processing helix chain 'B' and resid 1143 through 1177 removed outlier: 4.061A pdb=" N ARG B1177 " --> pdb=" O LYS B1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 4.413A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.585A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.675A pdb=" N ILE C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.545A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 removed outlier: 3.837A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 Processing helix chain 'C' and resid 606 through 633 Processing helix chain 'C' and resid 635 through 645 removed outlier: 3.513A pdb=" N ALA C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.852A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 862 removed outlier: 4.107A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 905 removed outlier: 3.503A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL C 912 " --> pdb=" O ILE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.833A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1088 removed outlier: 3.979A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1143 Processing helix chain 'C' and resid 1143 through 1177 removed outlier: 4.061A pdb=" N ARG C1177 " --> pdb=" O LYS C1173 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 4.412A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.584A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.675A pdb=" N ILE D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.546A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 removed outlier: 3.838A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 Processing helix chain 'D' and resid 606 through 633 Processing helix chain 'D' and resid 635 through 645 removed outlier: 3.514A pdb=" N ALA D 639 " --> pdb=" O GLU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.853A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 862 removed outlier: 4.107A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 905 removed outlier: 3.503A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL D 912 " --> pdb=" O ILE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS D 919 " --> pdb=" O GLN D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.834A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1088 removed outlier: 3.979A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1143 Processing helix chain 'D' and resid 1143 through 1177 removed outlier: 4.061A pdb=" N ARG D1177 " --> pdb=" O LYS D1173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 8.158A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.245A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 89 removed outlier: 8.157A pdb=" N TYR B 211 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.245A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 20 Processing sheet with id=AB1, first strand: chain 'C' and resid 88 through 89 removed outlier: 8.157A pdb=" N TYR C 211 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.245A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 89 removed outlier: 8.158A pdb=" N TYR D 211 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.245A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1916 hydrogen bonds defined for protein. 5568 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: 12.83 Time building geometry restraints manager: 14.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9708 1.34 - 1.46: 7319 1.46 - 1.58: 13373 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 30632 Sorted by residual: bond pdb=" N ALA C 189 " pdb=" CA ALA C 189 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.25e+00 bond pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.18e-02 7.18e+03 7.98e+00 bond pdb=" N ALA D 189 " pdb=" CA ALA D 189 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ALA B 189 " pdb=" CA ALA B 189 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ILE C 24 " pdb=" CA ILE C 24 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.32e+00 ... (remaining 30627 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.77: 957 106.77 - 113.68: 17422 113.68 - 120.59: 12779 120.59 - 127.50: 10102 127.50 - 134.41: 420 Bond angle restraints: 41680 Sorted by residual: angle pdb=" N PRO A 604 " pdb=" CA PRO A 604 " pdb=" C PRO A 604 " ideal model delta sigma weight residual 114.80 102.20 12.60 1.42e+00 4.96e-01 7.88e+01 angle pdb=" N PRO D 604 " pdb=" CA PRO D 604 " pdb=" C PRO D 604 " ideal model delta sigma weight residual 114.80 102.20 12.60 1.42e+00 4.96e-01 7.88e+01 angle pdb=" N PRO B 604 " pdb=" CA PRO B 604 " pdb=" C PRO B 604 " ideal model delta sigma weight residual 114.80 102.22 12.58 1.42e+00 4.96e-01 7.85e+01 angle pdb=" N PRO C 604 " pdb=" CA PRO C 604 " pdb=" C PRO C 604 " ideal model delta sigma weight residual 114.80 102.23 12.57 1.42e+00 4.96e-01 7.83e+01 angle pdb=" CA ASP B 605 " pdb=" C ASP B 605 " pdb=" O ASP B 605 " ideal model delta sigma weight residual 120.55 115.57 4.98 1.06e+00 8.90e-01 2.21e+01 ... (remaining 41675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 16700 15.87 - 31.73: 980 31.73 - 47.60: 192 47.60 - 63.46: 76 63.46 - 79.33: 16 Dihedral angle restraints: 17964 sinusoidal: 6620 harmonic: 11344 Sorted by residual: dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 37 " pdb=" CB CYS C 37 " ideal model delta sinusoidal sigma weight residual 93.00 141.27 -48.27 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS D 35 " pdb=" SG CYS D 35 " pdb=" SG CYS D 37 " pdb=" CB CYS D 37 " ideal model delta sinusoidal sigma weight residual 93.00 141.26 -48.26 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 37 " pdb=" CB CYS A 37 " ideal model delta sinusoidal sigma weight residual 93.00 141.26 -48.26 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 17961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3891 0.042 - 0.085: 705 0.085 - 0.127: 196 0.127 - 0.170: 9 0.170 - 0.212: 7 Chirality restraints: 4808 Sorted by residual: chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE C 24 " pdb=" N ILE C 24 " pdb=" C ILE C 24 " pdb=" CB ILE C 24 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE D 24 " pdb=" N ILE D 24 " pdb=" C ILE D 24 " pdb=" CB ILE D 24 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 4805 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 138 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LEU C 138 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU C 138 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 139 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 138 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU B 138 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU B 138 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 139 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 138 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU A 138 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 138 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 139 " -0.010 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 541 2.67 - 3.23: 31946 3.23 - 3.79: 48705 3.79 - 4.34: 60430 4.34 - 4.90: 100611 Nonbonded interactions: 242233 Sorted by model distance: nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.118 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.118 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.118 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.118 2.510 nonbonded pdb=" OD1 ASN C 865 " pdb="CA CA C2001 " model vdw 2.128 2.510 ... (remaining 242228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 84.220 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 30632 Z= 0.387 Angle : 0.627 12.605 41680 Z= 0.386 Chirality : 0.037 0.212 4808 Planarity : 0.004 0.036 5264 Dihedral : 11.398 79.326 10616 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.65 % Allowed : 5.52 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.14), residues: 3880 helix: 2.42 (0.10), residues: 2456 sheet: -0.13 (0.35), residues: 256 loop : -0.44 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.005 0.001 HIS D 173 PHE 0.009 0.001 PHE D 899 TYR 0.010 0.001 TYR A 577 ARG 0.003 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 3.447 Fit side-chains REVERT: A 625 ASP cc_start: 0.8983 (m-30) cc_final: 0.8720 (m-30) REVERT: A 877 LEU cc_start: 0.9601 (tt) cc_final: 0.9025 (tp) REVERT: B 284 MET cc_start: 0.7379 (mtp) cc_final: 0.6923 (mmt) REVERT: B 625 ASP cc_start: 0.8976 (m-30) cc_final: 0.8662 (m-30) REVERT: B 877 LEU cc_start: 0.9577 (tt) cc_final: 0.8976 (tp) REVERT: C 625 ASP cc_start: 0.8984 (m-30) cc_final: 0.8672 (m-30) REVERT: C 877 LEU cc_start: 0.9579 (tt) cc_final: 0.8978 (tp) REVERT: D 625 ASP cc_start: 0.8980 (m-30) cc_final: 0.8723 (m-30) REVERT: D 877 LEU cc_start: 0.9600 (tt) cc_final: 0.9029 (tp) outliers start: 19 outliers final: 4 residues processed: 203 average time/residue: 0.4077 time to fit residues: 137.4393 Evaluate side-chains 153 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain D residue 24 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 10.0000 chunk 300 optimal weight: 30.0000 chunk 166 optimal weight: 0.9990 chunk 102 optimal weight: 30.0000 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 669 GLN A 973 GLN A1051 GLN A1061 GLN B 240 HIS B 669 GLN B 973 GLN B1051 GLN B1061 GLN C 240 HIS C 669 GLN C 973 GLN C1051 GLN C1061 GLN D 240 HIS D 669 GLN D 973 GLN D1051 GLN D1061 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30632 Z= 0.352 Angle : 0.589 6.325 41680 Z= 0.297 Chirality : 0.038 0.128 4808 Planarity : 0.004 0.036 5264 Dihedral : 4.116 56.548 4272 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.06 % Allowed : 8.88 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.14), residues: 3880 helix: 2.55 (0.10), residues: 2492 sheet: 0.55 (0.35), residues: 244 loop : -0.59 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 191 HIS 0.004 0.001 HIS B 505 PHE 0.014 0.001 PHE D 627 TYR 0.007 0.001 TYR A 211 ARG 0.003 0.000 ARG D 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 3.762 Fit side-chains REVERT: A 284 MET cc_start: 0.7217 (mtp) cc_final: 0.6884 (mmt) REVERT: A 622 MET cc_start: 0.8329 (ttm) cc_final: 0.7816 (ttm) REVERT: A 625 ASP cc_start: 0.8935 (m-30) cc_final: 0.8659 (m-30) REVERT: A 926 MET cc_start: 0.9039 (mmt) cc_final: 0.8810 (mmt) REVERT: B 284 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6998 (mmt) REVERT: B 622 MET cc_start: 0.8341 (ttm) cc_final: 0.7811 (ttm) REVERT: B 625 ASP cc_start: 0.8931 (m-30) cc_final: 0.8661 (m-30) REVERT: C 284 MET cc_start: 0.7174 (mtp) cc_final: 0.6906 (mmt) REVERT: C 625 ASP cc_start: 0.8939 (m-30) cc_final: 0.8644 (m-30) REVERT: D 284 MET cc_start: 0.7225 (mtp) cc_final: 0.6869 (mmt) REVERT: D 622 MET cc_start: 0.8347 (ttm) cc_final: 0.7814 (ttm) REVERT: D 625 ASP cc_start: 0.8933 (m-30) cc_final: 0.8655 (m-30) outliers start: 31 outliers final: 12 residues processed: 178 average time/residue: 0.3496 time to fit residues: 109.5418 Evaluate side-chains 157 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 299 optimal weight: 0.0770 chunk 244 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 389 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30632 Z= 0.219 Angle : 0.494 6.749 41680 Z= 0.250 Chirality : 0.035 0.131 4808 Planarity : 0.004 0.042 5264 Dihedral : 3.679 23.650 4264 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.69 % Allowed : 10.67 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3880 helix: 2.69 (0.11), residues: 2496 sheet: 0.93 (0.39), residues: 208 loop : -0.63 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 772 HIS 0.003 0.001 HIS A 240 PHE 0.015 0.001 PHE D 627 TYR 0.006 0.001 TYR A 211 ARG 0.003 0.000 ARG C 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 3.475 Fit side-chains REVERT: A 284 MET cc_start: 0.7447 (mtp) cc_final: 0.6977 (mmt) REVERT: A 622 MET cc_start: 0.8301 (ttm) cc_final: 0.7956 (ttm) REVERT: A 625 ASP cc_start: 0.8926 (m-30) cc_final: 0.8648 (m-30) REVERT: B 284 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7013 (mmt) REVERT: B 622 MET cc_start: 0.8308 (ttm) cc_final: 0.7910 (ttm) REVERT: B 625 ASP cc_start: 0.8927 (m-30) cc_final: 0.8651 (m-30) REVERT: C 284 MET cc_start: 0.7423 (mtp) cc_final: 0.7026 (mmt) REVERT: C 622 MET cc_start: 0.8301 (ttm) cc_final: 0.7892 (ttm) REVERT: C 625 ASP cc_start: 0.8939 (m-30) cc_final: 0.8655 (m-30) REVERT: D 284 MET cc_start: 0.7438 (mtp) cc_final: 0.6967 (mmt) REVERT: D 622 MET cc_start: 0.8305 (ttm) cc_final: 0.7955 (ttm) REVERT: D 625 ASP cc_start: 0.8935 (m-30) cc_final: 0.8651 (m-30) outliers start: 20 outliers final: 8 residues processed: 160 average time/residue: 0.4417 time to fit residues: 121.0677 Evaluate side-chains 154 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 361 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN A1084 HIS B 116 ASN B 669 GLN B1084 HIS C 669 GLN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 HIS ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D1084 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30632 Z= 0.267 Angle : 0.524 6.851 41680 Z= 0.260 Chirality : 0.036 0.123 4808 Planarity : 0.004 0.045 5264 Dihedral : 3.661 23.453 4264 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.34 % Allowed : 11.32 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.14), residues: 3880 helix: 2.68 (0.10), residues: 2492 sheet: 0.05 (0.34), residues: 272 loop : -0.50 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1124 HIS 0.006 0.001 HIS D1084 PHE 0.014 0.001 PHE D 627 TYR 0.007 0.001 TYR C 577 ARG 0.004 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 3.423 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: A 284 MET cc_start: 0.7509 (mtp) cc_final: 0.7019 (mmt) REVERT: A 622 MET cc_start: 0.8351 (ttm) cc_final: 0.7961 (ttm) REVERT: A 625 ASP cc_start: 0.8919 (m-30) cc_final: 0.8655 (m-30) REVERT: A 1037 ASN cc_start: 0.8860 (m-40) cc_final: 0.8650 (m-40) REVERT: B 284 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7052 (mmt) REVERT: B 622 MET cc_start: 0.8364 (ttm) cc_final: 0.7989 (ttm) REVERT: B 625 ASP cc_start: 0.8921 (m-30) cc_final: 0.8661 (m-30) REVERT: B 1037 ASN cc_start: 0.8856 (m-40) cc_final: 0.8655 (m-40) REVERT: C 284 MET cc_start: 0.7451 (mtp) cc_final: 0.7024 (mmt) REVERT: C 581 MET cc_start: 0.8924 (mmp) cc_final: 0.8617 (mmp) REVERT: C 622 MET cc_start: 0.8331 (ttm) cc_final: 0.7958 (ttm) REVERT: C 625 ASP cc_start: 0.8916 (m-30) cc_final: 0.8663 (m-30) REVERT: D 284 MET cc_start: 0.7513 (mtp) cc_final: 0.7014 (mmt) REVERT: D 622 MET cc_start: 0.8369 (ttm) cc_final: 0.7985 (ttm) REVERT: D 625 ASP cc_start: 0.8919 (m-30) cc_final: 0.8656 (m-30) outliers start: 39 outliers final: 21 residues processed: 185 average time/residue: 0.3823 time to fit residues: 119.3626 Evaluate side-chains 172 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 326 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 343 optimal weight: 0.0270 chunk 96 optimal weight: 10.0000 overall best weight: 2.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 116 ASN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30632 Z= 0.198 Angle : 0.481 7.145 41680 Z= 0.241 Chirality : 0.035 0.119 4808 Planarity : 0.004 0.045 5264 Dihedral : 3.614 22.537 4264 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 12.38 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.14), residues: 3880 helix: 2.76 (0.10), residues: 2496 sheet: -0.52 (0.34), residues: 276 loop : -0.33 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 772 HIS 0.004 0.001 HIS B1002 PHE 0.014 0.001 PHE D 627 TYR 0.006 0.001 TYR A1063 ARG 0.003 0.000 ARG B1138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7049 (mmt) REVERT: A 576 MET cc_start: 0.9172 (tpp) cc_final: 0.8844 (tpp) REVERT: A 622 MET cc_start: 0.8363 (ttm) cc_final: 0.7974 (ttm) REVERT: A 625 ASP cc_start: 0.8908 (m-30) cc_final: 0.8657 (m-30) REVERT: B 284 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7012 (mmt) REVERT: B 576 MET cc_start: 0.9169 (tpp) cc_final: 0.8885 (tpp) REVERT: B 622 MET cc_start: 0.8347 (ttm) cc_final: 0.7984 (ttm) REVERT: B 625 ASP cc_start: 0.8893 (m-30) cc_final: 0.8617 (m-30) REVERT: C 284 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7086 (mmt) REVERT: C 576 MET cc_start: 0.9179 (tpp) cc_final: 0.8900 (tpp) REVERT: C 622 MET cc_start: 0.8333 (ttm) cc_final: 0.7967 (ttm) REVERT: C 625 ASP cc_start: 0.8907 (m-30) cc_final: 0.8650 (m-30) REVERT: D 284 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: D 576 MET cc_start: 0.9188 (tpp) cc_final: 0.8862 (tpp) REVERT: D 622 MET cc_start: 0.8370 (ttm) cc_final: 0.7981 (ttm) REVERT: D 625 ASP cc_start: 0.8908 (m-30) cc_final: 0.8645 (m-30) outliers start: 26 outliers final: 18 residues processed: 171 average time/residue: 0.3828 time to fit residues: 112.6506 Evaluate side-chains 165 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 0.0870 chunk 344 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 383 optimal weight: 4.9990 chunk 318 optimal weight: 30.0000 chunk 177 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 201 optimal weight: 30.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30632 Z= 0.284 Angle : 0.527 6.502 41680 Z= 0.260 Chirality : 0.035 0.117 4808 Planarity : 0.004 0.045 5264 Dihedral : 3.657 22.918 4264 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.34 % Allowed : 12.79 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.14), residues: 3880 helix: 2.74 (0.10), residues: 2504 sheet: -0.68 (0.32), residues: 276 loop : -0.23 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.002 0.001 HIS A 173 PHE 0.014 0.001 PHE B 627 TYR 0.007 0.001 TYR C 464 ARG 0.005 0.000 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 3.498 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: A 284 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7054 (mmt) REVERT: A 576 MET cc_start: 0.9210 (tpp) cc_final: 0.8869 (tpp) REVERT: A 622 MET cc_start: 0.8408 (ttm) cc_final: 0.7996 (ttm) REVERT: A 625 ASP cc_start: 0.8892 (m-30) cc_final: 0.8616 (m-30) REVERT: A 988 MET cc_start: 0.7578 (mtp) cc_final: 0.7018 (mtp) REVERT: B 284 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7099 (mmt) REVERT: B 576 MET cc_start: 0.9165 (tpp) cc_final: 0.8845 (tpp) REVERT: B 622 MET cc_start: 0.8401 (ttm) cc_final: 0.7993 (ttm) REVERT: B 625 ASP cc_start: 0.8892 (m-30) cc_final: 0.8617 (m-30) REVERT: B 988 MET cc_start: 0.7491 (mtp) cc_final: 0.7039 (mtp) REVERT: C 284 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: C 576 MET cc_start: 0.9168 (tpp) cc_final: 0.8856 (tpp) REVERT: C 622 MET cc_start: 0.8392 (ttm) cc_final: 0.7984 (ttm) REVERT: C 625 ASP cc_start: 0.8913 (m-30) cc_final: 0.8660 (m-30) REVERT: C 988 MET cc_start: 0.7474 (mtp) cc_final: 0.7262 (mtp) REVERT: D 284 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7050 (mmt) REVERT: D 576 MET cc_start: 0.9211 (tpp) cc_final: 0.8869 (tpp) REVERT: D 622 MET cc_start: 0.8424 (ttm) cc_final: 0.8015 (ttm) REVERT: D 625 ASP cc_start: 0.8912 (m-30) cc_final: 0.8652 (m-30) REVERT: D 988 MET cc_start: 0.7577 (mtp) cc_final: 0.7122 (mtp) outliers start: 39 outliers final: 31 residues processed: 171 average time/residue: 0.3705 time to fit residues: 110.0368 Evaluate side-chains 180 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1156 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 322 optimal weight: 30.0000 chunk 213 optimal weight: 0.6980 chunk 381 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30632 Z= 0.202 Angle : 0.482 6.647 41680 Z= 0.241 Chirality : 0.034 0.117 4808 Planarity : 0.004 0.047 5264 Dihedral : 3.593 22.140 4264 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.34 % Allowed : 13.07 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.14), residues: 3880 helix: 2.79 (0.10), residues: 2504 sheet: -0.70 (0.32), residues: 276 loop : -0.23 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 772 HIS 0.002 0.001 HIS D 240 PHE 0.017 0.001 PHE D 910 TYR 0.006 0.001 TYR B1063 ARG 0.003 0.000 ARG D1138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7052 (mmt) REVERT: A 576 MET cc_start: 0.9202 (tpp) cc_final: 0.8857 (tpp) REVERT: A 622 MET cc_start: 0.8402 (ttm) cc_final: 0.7995 (ttm) REVERT: A 625 ASP cc_start: 0.8885 (m-30) cc_final: 0.8605 (m-30) REVERT: B 284 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7096 (mmt) REVERT: B 576 MET cc_start: 0.9192 (tpp) cc_final: 0.8873 (tpp) REVERT: B 622 MET cc_start: 0.8387 (ttm) cc_final: 0.8031 (ttm) REVERT: B 625 ASP cc_start: 0.8882 (m-30) cc_final: 0.8605 (m-30) REVERT: C 284 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7130 (mmt) REVERT: C 576 MET cc_start: 0.9209 (tpp) cc_final: 0.8898 (tpp) REVERT: C 622 MET cc_start: 0.8384 (ttm) cc_final: 0.8005 (ttm) REVERT: C 625 ASP cc_start: 0.8876 (m-30) cc_final: 0.8606 (m-30) REVERT: D 284 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7066 (mmt) REVERT: D 576 MET cc_start: 0.9189 (tpp) cc_final: 0.8842 (tpp) REVERT: D 622 MET cc_start: 0.8381 (ttm) cc_final: 0.7982 (ttm) REVERT: D 625 ASP cc_start: 0.8888 (m-30) cc_final: 0.8632 (m-30) outliers start: 39 outliers final: 29 residues processed: 172 average time/residue: 0.3662 time to fit residues: 109.6460 Evaluate side-chains 179 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1156 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 300 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30632 Z= 0.247 Angle : 0.507 7.153 41680 Z= 0.251 Chirality : 0.035 0.116 4808 Planarity : 0.004 0.047 5264 Dihedral : 3.567 22.438 4264 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 1.17 % Allowed : 13.20 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.14), residues: 3880 helix: 2.80 (0.10), residues: 2504 sheet: -0.80 (0.32), residues: 276 loop : -0.21 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1124 HIS 0.002 0.001 HIS D 173 PHE 0.013 0.001 PHE D 627 TYR 0.006 0.001 TYR B1063 ARG 0.004 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 3.694 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: A 284 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: A 576 MET cc_start: 0.9199 (tpp) cc_final: 0.8845 (tpp) REVERT: A 622 MET cc_start: 0.8416 (ttm) cc_final: 0.7998 (ttm) REVERT: A 625 ASP cc_start: 0.8880 (m-30) cc_final: 0.8602 (m-30) REVERT: B 284 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7097 (mmt) REVERT: B 576 MET cc_start: 0.9194 (tpp) cc_final: 0.8864 (tpp) REVERT: B 622 MET cc_start: 0.8396 (ttm) cc_final: 0.8020 (ttm) REVERT: B 625 ASP cc_start: 0.8888 (m-30) cc_final: 0.8605 (m-30) REVERT: B 988 MET cc_start: 0.7380 (mtp) cc_final: 0.6748 (mtp) REVERT: C 284 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7127 (mmt) REVERT: C 576 MET cc_start: 0.9195 (tpp) cc_final: 0.8868 (tpp) REVERT: C 622 MET cc_start: 0.8418 (ttm) cc_final: 0.8013 (ttm) REVERT: C 625 ASP cc_start: 0.8874 (m-30) cc_final: 0.8594 (m-30) REVERT: C 988 MET cc_start: 0.7438 (mtp) cc_final: 0.6814 (mtp) REVERT: D 284 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: D 576 MET cc_start: 0.9208 (tpp) cc_final: 0.8844 (tpp) REVERT: D 622 MET cc_start: 0.8410 (ttm) cc_final: 0.7990 (ttm) REVERT: D 625 ASP cc_start: 0.8878 (m-30) cc_final: 0.8605 (m-30) outliers start: 34 outliers final: 29 residues processed: 162 average time/residue: 0.3539 time to fit residues: 98.8322 Evaluate side-chains 176 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1156 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 5.9990 chunk 365 optimal weight: 2.9990 chunk 333 optimal weight: 20.0000 chunk 355 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 154 optimal weight: 0.0970 chunk 279 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30632 Z= 0.154 Angle : 0.474 7.886 41680 Z= 0.237 Chirality : 0.034 0.117 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.528 21.229 4264 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.19 % Rotamer: Outliers : 1.17 % Allowed : 13.41 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.14), residues: 3880 helix: 2.81 (0.10), residues: 2516 sheet: -0.83 (0.32), residues: 280 loop : -0.24 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.005 0.001 HIS C 505 PHE 0.016 0.001 PHE D 910 TYR 0.005 0.001 TYR A1063 ARG 0.003 0.000 ARG D1138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7101 (mmt) REVERT: A 576 MET cc_start: 0.9185 (tpp) cc_final: 0.8878 (tpp) REVERT: A 622 MET cc_start: 0.8391 (ttm) cc_final: 0.8059 (ttm) REVERT: A 625 ASP cc_start: 0.8869 (m-30) cc_final: 0.8602 (m-30) REVERT: B 284 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7122 (mmt) REVERT: B 576 MET cc_start: 0.9202 (tpp) cc_final: 0.8915 (tpp) REVERT: B 622 MET cc_start: 0.8358 (ttm) cc_final: 0.8034 (ttm) REVERT: B 625 ASP cc_start: 0.8863 (m-30) cc_final: 0.8601 (m-30) REVERT: B 988 MET cc_start: 0.7237 (mtp) cc_final: 0.6629 (mtp) REVERT: C 284 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7105 (mmt) REVERT: C 576 MET cc_start: 0.9207 (tpp) cc_final: 0.8927 (tpp) REVERT: C 622 MET cc_start: 0.8374 (ttm) cc_final: 0.8007 (ttm) REVERT: C 625 ASP cc_start: 0.8861 (m-30) cc_final: 0.8586 (m-30) REVERT: C 988 MET cc_start: 0.7313 (mtp) cc_final: 0.6711 (mtp) REVERT: D 284 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7116 (mmt) REVERT: D 576 MET cc_start: 0.9188 (tpp) cc_final: 0.8882 (tpp) REVERT: D 622 MET cc_start: 0.8367 (ttm) cc_final: 0.8017 (ttm) REVERT: D 625 ASP cc_start: 0.8862 (m-30) cc_final: 0.8584 (m-30) outliers start: 34 outliers final: 26 residues processed: 166 average time/residue: 0.3541 time to fit residues: 102.1967 Evaluate side-chains 173 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 1.9990 chunk 376 optimal weight: 4.9990 chunk 229 optimal weight: 50.0000 chunk 178 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 394 optimal weight: 0.7980 chunk 363 optimal weight: 0.0060 chunk 314 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30632 Z= 0.169 Angle : 0.487 8.239 41680 Z= 0.241 Chirality : 0.034 0.185 4808 Planarity : 0.004 0.049 5264 Dihedral : 3.449 20.907 4264 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.98 % Rotamer: Outliers : 1.03 % Allowed : 13.58 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.14), residues: 3880 helix: 2.81 (0.10), residues: 2524 sheet: -0.89 (0.32), residues: 280 loop : -0.24 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 772 HIS 0.006 0.001 HIS D 505 PHE 0.012 0.001 PHE B 627 TYR 0.005 0.001 TYR C1063 ARG 0.005 0.000 ARG C 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7107 (mmt) REVERT: A 576 MET cc_start: 0.9196 (tpp) cc_final: 0.8887 (tpp) REVERT: A 622 MET cc_start: 0.8372 (ttm) cc_final: 0.8033 (ttm) REVERT: A 625 ASP cc_start: 0.8866 (m-30) cc_final: 0.8602 (m-30) REVERT: B 284 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7070 (mmt) REVERT: B 576 MET cc_start: 0.9198 (tpp) cc_final: 0.8912 (tpp) REVERT: B 622 MET cc_start: 0.8350 (ttm) cc_final: 0.8018 (ttm) REVERT: B 625 ASP cc_start: 0.8863 (m-30) cc_final: 0.8599 (m-30) REVERT: C 284 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7070 (mmt) REVERT: C 576 MET cc_start: 0.9204 (tpp) cc_final: 0.8920 (tpp) REVERT: C 622 MET cc_start: 0.8378 (ttm) cc_final: 0.8015 (ttm) REVERT: C 625 ASP cc_start: 0.8859 (m-30) cc_final: 0.8593 (m-30) REVERT: C 988 MET cc_start: 0.7268 (mtp) cc_final: 0.6703 (mtp) REVERT: D 284 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7128 (mmt) REVERT: D 576 MET cc_start: 0.9210 (tpp) cc_final: 0.8886 (tpp) REVERT: D 622 MET cc_start: 0.8375 (ttm) cc_final: 0.8024 (ttm) REVERT: D 625 ASP cc_start: 0.8857 (m-30) cc_final: 0.8595 (m-30) outliers start: 30 outliers final: 26 residues processed: 162 average time/residue: 0.3642 time to fit residues: 101.6161 Evaluate side-chains 171 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.065323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047460 restraints weight = 151460.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048947 restraints weight = 71627.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049992 restraints weight = 44915.208| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30632 Z= 0.340 Angle : 0.588 8.100 41680 Z= 0.287 Chirality : 0.036 0.174 4808 Planarity : 0.004 0.046 5264 Dihedral : 3.582 23.383 4264 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 1.20 % Allowed : 13.72 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.14), residues: 3880 helix: 2.77 (0.11), residues: 2520 sheet: -0.95 (0.31), residues: 272 loop : -0.27 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1124 HIS 0.004 0.001 HIS D 505 PHE 0.014 0.001 PHE D 783 TYR 0.010 0.001 TYR A 577 ARG 0.005 0.000 ARG D 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.51 seconds wall clock time: 88 minutes 8.60 seconds (5288.60 seconds total)