Starting phenix.real_space_refine on Sat Aug 10 15:38:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b94_44368/08_2024/9b94_44368.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b94_44368/08_2024/9b94_44368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b94_44368/08_2024/9b94_44368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b94_44368/08_2024/9b94_44368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b94_44368/08_2024/9b94_44368.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b94_44368/08_2024/9b94_44368.cif" } resolution = 3.1 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= 0.001 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 144 5.16 5 C 19128 2.51 5 N 5208 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7378 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 42, 'TRANS': 923} Chain breaks: 10 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 223 Chain: "B" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7378 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 42, 'TRANS': 923} Chain breaks: 10 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 223 Chain: "C" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7378 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 42, 'TRANS': 923} Chain breaks: 10 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 223 Chain: "D" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7378 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 42, 'TRANS': 923} Chain breaks: 10 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 223 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: 15.85, per 1000 atoms: 0.54 Number of scatterers: 29516 At special positions: 0 Unit cell: (163.116, 163.116, 158.976, 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 144 16.00 O 5032 8.00 N 5208 7.00 C 19128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.79 Conformation dependent library (CDL) restraints added in 5.6 seconds 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7168 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 67.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.989A pdb=" N LYS A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.904A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 174 removed outlier: 3.688A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.993A 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 317 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.976A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.638A 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: 4.012A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.547A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.890A 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 581 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.551A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.591A 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 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.625A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 915 through 926 removed outlier: 3.759A 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 974 removed outlier: 4.829A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.644A 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: 3.780A 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: 4.348A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1167 removed outlier: 3.519A pdb=" N GLU A1167 " --> pdb=" O GLY A1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 removed outlier: 3.989A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.903A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 174 removed outlier: 3.688A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.993A 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 317 Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.976A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.638A 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: 4.012A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.548A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.890A 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 581 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.550A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.590A 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 861 Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 905 removed outlier: 3.626A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 915 through 926 removed outlier: 3.759A 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 974 removed outlier: 4.829A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.644A 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: 3.781A 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: 4.348A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B1086 " --> pdb=" O ILE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1167 removed outlier: 3.519A pdb=" N GLU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 removed outlier: 3.990A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.903A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.687A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.993A 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 317 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.976A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.638A 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: 4.011A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.547A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.889A 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 581 Processing helix chain 'C' and resid 584 through 602 Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.551A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.591A 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 861 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 905 removed outlier: 3.625A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 915 through 926 removed outlier: 3.759A 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 974 removed outlier: 4.829A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.644A 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: 3.780A 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: 4.348A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C1086 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1167 removed outlier: 3.519A pdb=" N GLU C1167 " --> pdb=" O GLY C1163 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 removed outlier: 3.989A pdb=" N LYS D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.904A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 174 removed outlier: 3.688A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.992A 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 317 Processing helix chain 'D' and resid 329 through 337 Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.977A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.637A 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: 4.011A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.547A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.889A 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 581 Processing helix chain 'D' and resid 584 through 602 Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.551A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.590A 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 861 Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 905 removed outlier: 3.625A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 915 through 926 removed outlier: 3.758A 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 974 removed outlier: 4.829A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.645A 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: 3.780A 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: 4.348A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D1086 " --> pdb=" O ILE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1167 removed outlier: 3.518A pdb=" N GLU D1167 " --> pdb=" O GLY D1163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 3.851A pdb=" N THR A 68 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.098A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.245A 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: 8.349A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.851A pdb=" N THR B 68 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.097A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.245A 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: 8.349A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B1000 " --> pdb=" O SER B 991 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 removed outlier: 3.851A pdb=" N THR C 68 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.969A pdb=" N GLY C 76 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.098A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP C1000 " --> pdb=" O SER C 991 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.852A pdb=" N THR D 68 " --> pdb=" O THR D 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.969A pdb=" N GLY D 76 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.097A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP D1000 " --> pdb=" O SER D 991 " (cutoff:3.500A) 1830 hydrogen bonds defined for protein. 5298 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: 10.70 Time building geometry restraints manager: 12.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9564 1.34 - 1.46: 7176 1.46 - 1.58: 13228 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 30188 Sorted by residual: bond pdb=" N ASP C 605 " pdb=" CA ASP C 605 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.29e+00 bond pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N ASP B 605 " pdb=" CA ASP B 605 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N ASP D 605 " pdb=" CA ASP D 605 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.91e+00 bond pdb=" N GLU C 607 " pdb=" CA GLU C 607 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.61e+00 ... (remaining 30183 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 917 106.58 - 113.44: 16750 113.44 - 120.29: 11194 120.29 - 127.15: 11749 127.15 - 134.01: 438 Bond angle restraints: 41048 Sorted by residual: angle pdb=" C THR D 21 " pdb=" CA THR D 21 " pdb=" CB THR D 21 " ideal model delta sigma weight residual 116.63 112.18 4.45 1.16e+00 7.43e-01 1.47e+01 angle pdb=" C THR A 21 " pdb=" CA THR A 21 " pdb=" CB THR A 21 " ideal model delta sigma weight residual 116.63 112.21 4.42 1.16e+00 7.43e-01 1.45e+01 angle pdb=" C THR C 21 " pdb=" CA THR C 21 " pdb=" CB THR C 21 " ideal model delta sigma weight residual 116.63 112.22 4.41 1.16e+00 7.43e-01 1.45e+01 angle pdb=" C THR B 21 " pdb=" CA THR B 21 " pdb=" CB THR B 21 " ideal model delta sigma weight residual 116.63 112.24 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" CA THR D 19 " pdb=" CB THR D 19 " pdb=" OG1 THR D 19 " ideal model delta sigma weight residual 109.60 104.55 5.05 1.50e+00 4.44e-01 1.13e+01 ... (remaining 41043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 16845 17.25 - 34.49: 699 34.49 - 51.74: 124 51.74 - 68.99: 36 68.99 - 86.24: 12 Dihedral angle restraints: 17716 sinusoidal: 6640 harmonic: 11076 Sorted by residual: dihedral pdb=" CB GLU B 608 " pdb=" CG GLU B 608 " pdb=" CD GLU B 608 " pdb=" OE1 GLU B 608 " ideal model delta sinusoidal sigma weight residual 0.00 -86.24 86.24 1 3.00e+01 1.11e-03 9.97e+00 dihedral pdb=" CB GLU D 608 " pdb=" CG GLU D 608 " pdb=" CD GLU D 608 " pdb=" OE1 GLU D 608 " ideal model delta sinusoidal sigma weight residual 0.00 -86.21 86.21 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU A 608 " pdb=" CG GLU A 608 " pdb=" CD GLU A 608 " pdb=" OE1 GLU A 608 " ideal model delta sinusoidal sigma weight residual 0.00 -86.20 86.20 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 17713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3178 0.028 - 0.057: 1065 0.057 - 0.085: 311 0.085 - 0.113: 141 0.113 - 0.141: 25 Chirality restraints: 4720 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE D 271 " pdb=" N ILE D 271 " pdb=" C ILE D 271 " pdb=" CB ILE D 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE C 271 " pdb=" N ILE C 271 " pdb=" C ILE C 271 " pdb=" CB ILE C 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 4717 not shown) Planarity restraints: 5176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1076 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO D1077 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D1077 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1077 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1076 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO C1077 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C1077 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1077 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A1077 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.020 5.00e-02 4.00e+02 ... (remaining 5173 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 3233 2.74 - 3.28: 31194 3.28 - 3.82: 50332 3.82 - 4.36: 56807 4.36 - 4.90: 100827 Nonbonded interactions: 242393 Sorted by model distance: nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.194 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.194 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.195 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.195 2.510 nonbonded pdb=" OE1 GLN C 831 " pdb="CA CA C2001 " model vdw 2.235 2.510 ... (remaining 242388 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.290 Process input model: 76.180 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.120 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 : 0.004 0.035 30188 Z= 0.286 Angle : 0.493 5.997 41048 Z= 0.287 Chirality : 0.034 0.141 4720 Planarity : 0.003 0.036 5176 Dihedral : 10.724 86.236 10548 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.82 % Allowed : 4.25 % Favored : 94.92 % 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: 2.22 (0.15), residues: 3776 helix: 2.66 (0.11), residues: 2376 sheet: -1.28 (0.32), residues: 284 loop : -0.41 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1124 HIS 0.004 0.001 HIS C1128 PHE 0.010 0.001 PHE C 627 TYR 0.007 0.001 TYR C 968 ARG 0.002 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 509 MET cc_start: 0.8644 (tmm) cc_final: 0.8422 (tmm) outliers start: 24 outliers final: 6 residues processed: 127 average time/residue: 0.4062 time to fit residues: 84.8651 Evaluate side-chains 97 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 9.9990 chunk 291 optimal weight: 50.0000 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.0570 chunk 196 optimal weight: 0.0070 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 30.0000 chunk 348 optimal weight: 7.9990 overall best weight: 2.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 GLN B 973 GLN C 973 GLN D 295 GLN D 973 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30188 Z= 0.228 Angle : 0.508 6.472 41048 Z= 0.259 Chirality : 0.036 0.141 4720 Planarity : 0.004 0.047 5176 Dihedral : 4.059 61.516 4178 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.45 % Allowed : 5.42 % Favored : 94.14 % 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: 2.25 (0.15), residues: 3776 helix: 2.67 (0.11), residues: 2388 sheet: -1.38 (0.32), residues: 284 loop : -0.37 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.003 0.001 HIS D1128 PHE 0.011 0.001 PHE C 627 TYR 0.009 0.001 TYR D 211 ARG 0.005 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 3.296 Fit side-chains REVERT: A 355 MET cc_start: 0.8968 (mmm) cc_final: 0.8762 (mmm) REVERT: A 603 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: C 355 MET cc_start: 0.9085 (mmm) cc_final: 0.8875 (mmm) REVERT: D 355 MET cc_start: 0.8974 (mmm) cc_final: 0.8766 (mmm) REVERT: D 509 MET cc_start: 0.8694 (tmm) cc_final: 0.8456 (tmm) REVERT: D 603 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7674 (tt0) outliers start: 13 outliers final: 4 residues processed: 96 average time/residue: 0.3826 time to fit residues: 64.6448 Evaluate side-chains 94 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 50.0000 chunk 108 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 349 optimal weight: 6.9990 chunk 377 optimal weight: 0.6980 chunk 311 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 30188 Z= 0.405 Angle : 0.559 6.769 41048 Z= 0.281 Chirality : 0.038 0.132 4720 Planarity : 0.004 0.054 5176 Dihedral : 4.102 56.198 4178 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.03 % Allowed : 6.31 % Favored : 92.66 % 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: 2.10 (0.14), residues: 3776 helix: 2.53 (0.11), residues: 2400 sheet: -1.09 (0.33), residues: 256 loop : -0.52 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1124 HIS 0.006 0.001 HIS D1128 PHE 0.014 0.001 PHE B1069 TYR 0.009 0.001 TYR C 464 ARG 0.004 0.000 ARG D1147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 3.509 Fit side-chains REVERT: A 355 MET cc_start: 0.8933 (mmm) cc_final: 0.8725 (mmm) REVERT: A 637 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8433 (ptp-170) REVERT: C 355 MET cc_start: 0.9054 (mmm) cc_final: 0.8832 (mmm) REVERT: D 355 MET cc_start: 0.8947 (mmm) cc_final: 0.8711 (mmm) outliers start: 30 outliers final: 13 residues processed: 105 average time/residue: 0.3927 time to fit residues: 71.0273 Evaluate side-chains 100 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 181 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 371 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 332 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30188 Z= 0.173 Angle : 0.462 6.955 41048 Z= 0.234 Chirality : 0.035 0.133 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.685 22.176 4172 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 7.10 % Favored : 91.80 % 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: 2.23 (0.14), residues: 3776 helix: 2.66 (0.11), residues: 2392 sheet: -1.32 (0.32), residues: 284 loop : -0.43 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.003 0.000 HIS D1128 PHE 0.012 0.001 PHE D 899 TYR 0.007 0.001 TYR A 211 ARG 0.002 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 3.225 Fit side-chains REVERT: A 637 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8484 (ptp-170) REVERT: B 509 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8581 (tmm) REVERT: C 355 MET cc_start: 0.9025 (mmm) cc_final: 0.8817 (mmm) REVERT: D 284 MET cc_start: 0.8807 (mmt) cc_final: 0.8599 (mmt) REVERT: D 355 MET cc_start: 0.8887 (mmm) cc_final: 0.8659 (mmm) outliers start: 32 outliers final: 18 residues processed: 107 average time/residue: 0.3927 time to fit residues: 72.5531 Evaluate side-chains 106 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 256 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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: 0.8909 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30188 Z= 0.213 Angle : 0.462 6.990 41048 Z= 0.233 Chirality : 0.035 0.131 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.621 22.306 4172 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 1.23 % Allowed : 7.92 % Favored : 90.84 % 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: 2.27 (0.14), residues: 3776 helix: 2.70 (0.11), residues: 2392 sheet: -1.31 (0.32), residues: 284 loop : -0.45 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1124 HIS 0.007 0.001 HIS D 505 PHE 0.012 0.001 PHE C 627 TYR 0.007 0.001 TYR B 464 ARG 0.003 0.000 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 3.384 Fit side-chains REVERT: A 186 MET cc_start: 0.9057 (mpp) cc_final: 0.8784 (mpp) REVERT: A 637 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8453 (ptp-170) REVERT: B 355 MET cc_start: 0.8912 (mmm) cc_final: 0.8653 (mmm) REVERT: C 355 MET cc_start: 0.8996 (mmm) cc_final: 0.8792 (mmm) REVERT: D 355 MET cc_start: 0.8912 (mmm) cc_final: 0.8683 (mmm) outliers start: 36 outliers final: 27 residues processed: 109 average time/residue: 0.3664 time to fit residues: 70.3019 Evaluate side-chains 112 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 195 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8927 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 30188 Z= 0.296 Angle : 0.496 7.184 41048 Z= 0.249 Chirality : 0.036 0.128 4720 Planarity : 0.004 0.053 5176 Dihedral : 3.647 23.587 4172 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 1.27 % Allowed : 8.40 % Favored : 90.33 % 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: 2.25 (0.14), residues: 3776 helix: 2.67 (0.11), residues: 2400 sheet: -1.26 (0.32), residues: 284 loop : -0.43 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS D1128 PHE 0.013 0.001 PHE C 627 TYR 0.008 0.001 TYR B 464 ARG 0.002 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 3.276 Fit side-chains REVERT: A 186 MET cc_start: 0.9044 (mpp) cc_final: 0.8741 (mpp) REVERT: A 637 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8409 (ptp-170) REVERT: B 355 MET cc_start: 0.8987 (mmm) cc_final: 0.8689 (mmm) REVERT: C 355 MET cc_start: 0.9006 (mmm) cc_final: 0.8802 (mmm) REVERT: D 355 MET cc_start: 0.8893 (mmm) cc_final: 0.8659 (mmm) outliers start: 37 outliers final: 26 residues processed: 111 average time/residue: 0.3593 time to fit residues: 69.8862 Evaluate side-chains 111 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 271 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 370 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30188 Z= 0.224 Angle : 0.463 7.265 41048 Z= 0.234 Chirality : 0.035 0.130 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.633 23.031 4172 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 1.23 % Allowed : 8.85 % Favored : 89.92 % 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: 2.29 (0.15), residues: 3776 helix: 2.71 (0.11), residues: 2392 sheet: -1.24 (0.32), residues: 284 loop : -0.42 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1124 HIS 0.004 0.001 HIS D1128 PHE 0.012 0.001 PHE C 627 TYR 0.007 0.001 TYR B 464 ARG 0.002 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 3.385 Fit side-chains REVERT: A 637 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8446 (ptp-170) REVERT: B 355 MET cc_start: 0.9008 (mmm) cc_final: 0.8696 (mmm) REVERT: D 355 MET cc_start: 0.8922 (mmm) cc_final: 0.8694 (mmm) outliers start: 36 outliers final: 26 residues processed: 110 average time/residue: 0.3940 time to fit residues: 75.4778 Evaluate side-chains 111 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 0.0070 chunk 252 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 290 optimal weight: 0.9980 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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: 0.8894 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30188 Z= 0.165 Angle : 0.442 8.116 41048 Z= 0.224 Chirality : 0.035 0.133 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.559 21.604 4172 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 1.20 % Allowed : 9.09 % Favored : 89.71 % 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 (0.15), residues: 3776 helix: 2.72 (0.11), residues: 2400 sheet: -1.67 (0.33), residues: 264 loop : -0.34 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.003 0.000 HIS D1128 PHE 0.012 0.001 PHE A 899 TYR 0.006 0.001 TYR C 464 ARG 0.002 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 3.439 Fit side-chains REVERT: A 637 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8523 (ptp-170) REVERT: B 355 MET cc_start: 0.8986 (mmm) cc_final: 0.8680 (mmm) REVERT: C 355 MET cc_start: 0.8894 (mmm) cc_final: 0.8518 (mmm) REVERT: D 186 MET cc_start: 0.9110 (mmm) cc_final: 0.8821 (mpp) REVERT: D 355 MET cc_start: 0.8923 (mmm) cc_final: 0.8702 (mmm) REVERT: D 430 MET cc_start: 0.9178 (mmt) cc_final: 0.8865 (mmm) outliers start: 35 outliers final: 29 residues processed: 112 average time/residue: 0.3732 time to fit residues: 72.8049 Evaluate side-chains 114 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8898 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30188 Z= 0.186 Angle : 0.454 11.343 41048 Z= 0.228 Chirality : 0.035 0.131 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.517 21.629 4172 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 1.17 % Allowed : 9.16 % Favored : 89.68 % 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: 2.34 (0.15), residues: 3776 helix: 2.75 (0.11), residues: 2396 sheet: -1.63 (0.33), residues: 264 loop : -0.35 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 579 HIS 0.003 0.000 HIS A1128 PHE 0.012 0.001 PHE A 627 TYR 0.007 0.001 TYR C 464 ARG 0.001 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 3.244 Fit side-chains REVERT: A 637 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8509 (ptp-170) REVERT: B 355 MET cc_start: 0.9003 (mmm) cc_final: 0.8686 (mmm) REVERT: C 355 MET cc_start: 0.8886 (mmm) cc_final: 0.8468 (mmm) REVERT: D 186 MET cc_start: 0.9100 (mmm) cc_final: 0.8763 (mpp) REVERT: D 355 MET cc_start: 0.8918 (mmm) cc_final: 0.8699 (mmm) outliers start: 34 outliers final: 31 residues processed: 112 average time/residue: 0.3674 time to fit residues: 72.2717 Evaluate side-chains 116 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.0870 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 382 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 304 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 235 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 overall best weight: 3.6164 ------------------------------------------------------------------------------- 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: 0.8917 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30188 Z= 0.250 Angle : 0.481 11.885 41048 Z= 0.240 Chirality : 0.035 0.128 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.548 23.035 4172 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 1.13 % Allowed : 9.12 % Favored : 89.75 % 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: 2.36 (0.15), residues: 3776 helix: 2.75 (0.11), residues: 2396 sheet: -1.20 (0.32), residues: 284 loop : -0.38 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 579 HIS 0.004 0.001 HIS A1128 PHE 0.013 0.001 PHE C 627 TYR 0.008 0.001 TYR C 464 ARG 0.002 0.000 ARG D 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 3.476 Fit side-chains REVERT: A 637 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8460 (ptp-170) REVERT: B 355 MET cc_start: 0.9018 (mmm) cc_final: 0.8703 (mmm) REVERT: C 355 MET cc_start: 0.8908 (mmm) cc_final: 0.8521 (mmm) REVERT: D 186 MET cc_start: 0.9090 (mmm) cc_final: 0.8690 (mpp) REVERT: D 355 MET cc_start: 0.8932 (mmm) cc_final: 0.8708 (mmm) outliers start: 33 outliers final: 32 residues processed: 110 average time/residue: 0.3658 time to fit residues: 71.4798 Evaluate side-chains 117 residues out of total 3260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.9990 chunk 324 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 305 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 313 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.054377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.039467 restraints weight = 159920.291| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.39 r_work: 0.2799 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30188 Z= 0.163 Angle : 0.445 14.086 41048 Z= 0.224 Chirality : 0.034 0.133 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.506 21.514 4172 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % Rotamer: Outliers : 1.10 % Allowed : 9.19 % Favored : 89.71 % 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: 2.39 (0.15), residues: 3776 helix: 2.73 (0.11), residues: 2408 sheet: -1.15 (0.32), residues: 284 loop : -0.31 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1124 HIS 0.003 0.000 HIS A1128 PHE 0.012 0.001 PHE A 899 TYR 0.006 0.001 TYR D 464 ARG 0.002 0.000 ARG D 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.87 seconds wall clock time: 88 minutes 37.58 seconds (5317.58 seconds total)