Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 17:37:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymy_33947/10_2023/7ymy_33947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymy_33947/10_2023/7ymy_33947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymy_33947/10_2023/7ymy_33947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymy_33947/10_2023/7ymy_33947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymy_33947/10_2023/7ymy_33947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymy_33947/10_2023/7ymy_33947.pdb" } resolution = 4.96 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= -0.005 sd= 0.118 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17546 2.51 5 N 4504 2.21 5 O 5474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "B TYR 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 27677 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.43, per 1000 atoms: 0.52 Number of scatterers: 27677 At special positions: 0 Unit cell: (155.1, 161.7, 179.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5474 8.00 N 4504 7.00 C 17546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.04 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.02 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.02 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.04 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A1401 " - " ASN A 166 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 619 " " NAG A1404 " - " ASN A 719 " " NAG A1405 " - " ASN A 785 " " NAG A1406 " - " ASN A 870 " " NAG A1407 " - " ASN A1213 " " NAG B1401 " - " ASN B 719 " " NAG B1402 " - " ASN B 785 " " NAG B1403 " - " ASN B 870 " " NAG B1404 " - " ASN B 619 " " NAG B1405 " - " ASN B1213 " " NAG C1401 " - " ASN C 619 " " NAG C1402 " - " ASN C1213 " " NAG C1403 " - " ASN C 166 " " NAG C1404 " - " ASN C 870 " " NAG C1405 " - " ASN C 719 " " NAG C1406 " - " ASN C 236 " " NAG C1407 " - " ASN C 785 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN B 125 " " NAG H 1 " - " ASN B 222 " " NAG I 1 " - " ASN B 66 " " NAG J 1 " - " ASN C 66 " " NAG K 1 " - " ASN C 222 " " NAG L 1 " - " ASN C 125 " Time building additional restraints: 11.96 Conformation dependent library (CDL) restraints added in 3.8 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 25.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.797A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 218 through 221 removed outlier: 4.216A pdb=" N ARG A 221 " --> pdb=" O ASN A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.883A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.776A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.577A pdb=" N LEU A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A 416 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.706A pdb=" N ILE A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A 434 " --> pdb=" O ALA A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.543A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.950A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.910A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 removed outlier: 3.618A pdb=" N TYR A 809 " --> pdb=" O ASP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.671A pdb=" N ARG A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 854 removed outlier: 3.978A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 896 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.770A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.613A pdb=" N LEU A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 Processing helix chain 'A' and resid 1016 through 1039 removed outlier: 3.699A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.096A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.849A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.801A pdb=" N ARG B 221 " --> pdb=" O ASN B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 4.012A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.259A pdb=" N ILE B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.253A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.760A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.100A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 removed outlier: 3.835A pdb=" N ARG B 822 " --> pdb=" O GLU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 915 Processing helix chain 'B' and resid 924 through 930 removed outlier: 4.166A pdb=" N TYR B 928 " --> pdb=" O CYS B 925 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 930 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 959 removed outlier: 3.691A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.516A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 4.005A pdb=" N GLN B1020 " --> pdb=" O ASN B1016 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.714A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.762A pdb=" N GLN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.793A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.531A pdb=" N LYS C 413 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.724A pdb=" N MET C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.792A pdb=" N LYS C 595 " --> pdb=" O ASN C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.772A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 814 through 825 removed outlier: 4.113A pdb=" N ARG C 822 " --> pdb=" O GLU C 818 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 854 removed outlier: 3.761A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 909 through 914 Processing helix chain 'C' and resid 940 through 956 Processing helix chain 'C' and resid 971 through 984 removed outlier: 3.599A pdb=" N SER C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.608A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1011 removed outlier: 3.867A pdb=" N ILE C 997 " --> pdb=" O ASN C 993 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C1011 " --> pdb=" O ALA C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1038 removed outlier: 3.652A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1041 No H-bonds generated for 'chain 'C' and resid 1039 through 1041' Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.544A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C1106 " --> pdb=" O LYS C1102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.141A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.507A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.566A pdb=" N LYS A 110 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 284 removed outlier: 5.271A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 155 removed outlier: 4.679A pdb=" N SER A 152 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.698A pdb=" N GLY A 372 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A 607 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.698A pdb=" N GLY A 372 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A 607 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 648 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.136A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.659A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 659 through 664 removed outlier: 4.098A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 724 removed outlier: 6.333A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.161A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 782 removed outlier: 4.767A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 795 removed outlier: 5.563A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 3.683A pdb=" N ILE A1214 " --> pdb=" O CYS A1156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1167 Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.498A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.748A pdb=" N TYR B 314 " --> pdb=" O ARG B 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.148A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.182A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC8, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AC9, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.763A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 372 through 373 removed outlier: 6.974A pdb=" N GLY B 372 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N SER B 607 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 400 through 404 Processing sheet with id=AD3, first strand: chain 'B' and resid 407 through 409 removed outlier: 3.690A pdb=" N CYS B 585 " --> pdb=" O CYS B 407 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 513 through 515 removed outlier: 4.809A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 724 removed outlier: 3.617A pdb=" N VAL B 718 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 720 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 722 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.477A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 778 through 795 removed outlier: 6.449A pdb=" N ASN B1145 " --> pdb=" O THR B 784 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B 786 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE B 788 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR B1141 " --> pdb=" O PHE B 788 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 790 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1139 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN B 792 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET B1137 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 794 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B1135 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD9, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 3.664A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1170 through 1174 Processing sheet with id=AE2, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.262A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.353A pdb=" N VAL C 263 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 283 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 279 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.881A pdb=" N LYS C 110 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 147 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 126 through 129 removed outlier: 3.881A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 152 through 155 removed outlier: 4.222A pdb=" N SER C 152 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.952A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AF1, first strand: chain 'C' and resid 403 through 404 removed outlier: 6.347A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 514 removed outlier: 6.903A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.054A pdb=" N TYR C 648 " --> pdb=" O CYS C 620 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 719 through 724 removed outlier: 5.589A pdb=" N LEU C 759 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU C 722 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 778 through 782 removed outlier: 4.648A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 785 through 796 removed outlier: 6.067A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 802 through 804 removed outlier: 3.529A pdb=" N LYS C 933 " --> pdb=" O THR C 803 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1155 through 1156 removed outlier: 3.831A pdb=" N LEU C1155 " --> pdb=" O ILE C1165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C1165 " --> pdb=" O LEU C1155 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2736 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: 12.36 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6005 1.33 - 1.46: 8085 1.46 - 1.58: 14013 1.58 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 28307 Sorted by residual: bond pdb=" CA ARG C 221 " pdb=" C ARG C 221 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.34e-02 5.57e+03 6.02e+01 bond pdb=" CA TYR B 270 " pdb=" C TYR B 270 " ideal model delta sigma weight residual 1.523 1.425 0.098 1.35e-02 5.49e+03 5.26e+01 bond pdb=" CA SER B 268 " pdb=" C SER B 268 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.11e-02 8.12e+03 4.52e+01 bond pdb=" CA ASN C 220 " pdb=" C ASN C 220 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.34e-02 5.57e+03 3.80e+01 bond pdb=" N VAL B 271 " pdb=" CA VAL B 271 " ideal model delta sigma weight residual 1.457 1.388 0.069 1.29e-02 6.01e+03 2.88e+01 ... (remaining 28302 not shown) Histogram of bond angle deviations from ideal: 97.55 - 105.44: 606 105.44 - 113.33: 15413 113.33 - 121.22: 14647 121.22 - 129.11: 7737 129.11 - 137.00: 106 Bond angle restraints: 38509 Sorted by residual: angle pdb=" N ARG B 269 " pdb=" CA ARG B 269 " pdb=" C ARG B 269 " ideal model delta sigma weight residual 111.40 100.13 11.27 1.22e+00 6.72e-01 8.54e+01 angle pdb=" N GLY A 866 " pdb=" CA GLY A 866 " pdb=" C GLY A 866 " ideal model delta sigma weight residual 114.67 102.29 12.38 1.41e+00 5.03e-01 7.71e+01 angle pdb=" C ILE C 57 " pdb=" N TYR C 58 " pdb=" CA TYR C 58 " ideal model delta sigma weight residual 120.68 132.57 -11.89 1.52e+00 4.33e-01 6.12e+01 angle pdb=" N LYS A 453 " pdb=" CA LYS A 453 " pdb=" C LYS A 453 " ideal model delta sigma weight residual 111.75 120.37 -8.62 1.28e+00 6.10e-01 4.54e+01 angle pdb=" C GLN A 319 " pdb=" N PRO A 320 " pdb=" CA PRO A 320 " ideal model delta sigma weight residual 119.90 113.62 6.28 1.05e+00 9.07e-01 3.57e+01 ... (remaining 38504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14795 17.99 - 35.99: 1392 35.99 - 53.98: 240 53.98 - 71.97: 57 71.97 - 89.97: 46 Dihedral angle restraints: 16530 sinusoidal: 6339 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -162.44 76.44 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -162.43 76.43 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS A 811 " pdb=" SG CYS A 811 " pdb=" SG CYS A 817 " pdb=" CB CYS A 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.96 74.96 1 1.00e+01 1.00e-02 7.11e+01 ... (remaining 16527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 4417 0.213 - 0.426: 20 0.426 - 0.639: 2 0.639 - 0.853: 0 0.853 - 1.066: 3 Chirality restraints: 4442 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 125 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 222 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 125 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 4439 not shown) Planarity restraints: 4961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 875 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 876 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 876 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 876 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1059 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO C1060 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C1060 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C1060 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 902 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 903 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 903 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 903 " -0.047 5.00e-02 4.00e+02 ... (remaining 4958 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2890 2.74 - 3.28: 29272 3.28 - 3.82: 50296 3.82 - 4.36: 56709 4.36 - 4.90: 90998 Nonbonded interactions: 230165 Sorted by model distance: nonbonded pdb=" O PRO B 525 " pdb=" OG SER B 528 " model vdw 2.203 2.440 nonbonded pdb=" OG SER C 643 " pdb=" OD1 ASP C 645 " model vdw 2.205 2.440 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR A 397 " pdb=" O PRO A 531 " model vdw 2.212 2.440 nonbonded pdb=" NE2 GLN B 427 " pdb=" O ASN B 475 " model vdw 2.213 2.520 ... (remaining 230160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1223 or resid 1401 through 1405)) selection = chain 'B' selection = (chain 'C' and (resid 19 through 1223 or resid 1401 through 1405)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'L' } 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: 1.160 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: 5.280 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 74.250 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.210 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.104 28307 Z= 0.376 Angle : 0.959 12.381 38509 Z= 0.514 Chirality : 0.064 1.066 4442 Planarity : 0.007 0.106 4933 Dihedral : 14.842 89.968 9876 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.64 % Favored : 91.19 % Rotamer: Outliers : 0.50 % Allowed : 0.80 % Favored : 98.70 % Cbeta Deviations : 0.09 % 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: -2.07 (0.13), residues: 3462 helix: -0.35 (0.19), residues: 697 sheet: -1.16 (0.18), residues: 728 loop : -1.88 (0.13), residues: 2037 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 147 average time/residue: 0.3975 time to fit residues: 94.2912 Evaluate side-chains 92 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 3.016 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.4931 time to fit residues: 8.2008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 40.0000 chunk 263 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 177 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 203 optimal weight: 50.0000 chunk 316 optimal weight: 9.9990 overall best weight: 11.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN A 974 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN A1145 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 812 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN C 836 HIS ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1208 GLN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28307 Z= 0.338 Angle : 0.731 11.113 38509 Z= 0.384 Chirality : 0.047 0.640 4442 Planarity : 0.006 0.068 4933 Dihedral : 5.822 24.435 3786 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 30.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.13 % Allowed : 7.34 % Favored : 92.52 % 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: -1.89 (0.14), residues: 3462 helix: 0.14 (0.19), residues: 703 sheet: -1.39 (0.18), residues: 765 loop : -1.75 (0.13), residues: 1994 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.3927 time to fit residues: 64.9952 Evaluate side-chains 79 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2630 time to fit residues: 5.2992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 215 optimal weight: 40.0000 chunk 87 optimal weight: 0.5980 chunk 316 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 208 HIS ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28307 Z= 0.183 Angle : 0.611 8.209 38509 Z= 0.314 Chirality : 0.045 0.559 4442 Planarity : 0.005 0.060 4933 Dihedral : 5.474 27.534 3786 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.65 % 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: -1.74 (0.14), residues: 3462 helix: 0.34 (0.19), residues: 715 sheet: -1.32 (0.18), residues: 728 loop : -1.68 (0.13), residues: 2019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.3758 time to fit residues: 59.1846 Evaluate side-chains 77 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 3.023 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2786 time to fit residues: 4.5151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 151 optimal weight: 50.0000 chunk 212 optimal weight: 10.0000 chunk 317 optimal weight: 50.0000 chunk 336 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 chunk 90 optimal weight: 0.3980 overall best weight: 9.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN A 842 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28307 Z= 0.281 Angle : 0.647 8.450 38509 Z= 0.339 Chirality : 0.046 0.618 4442 Planarity : 0.005 0.061 4933 Dihedral : 5.507 23.789 3786 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % 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: -1.79 (0.14), residues: 3462 helix: 0.31 (0.19), residues: 710 sheet: -1.45 (0.18), residues: 724 loop : -1.68 (0.13), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.3968 time to fit residues: 61.6588 Evaluate side-chains 78 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 3.461 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2914 time to fit residues: 4.9810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 250 optimal weight: 50.0000 chunk 138 optimal weight: 3.9990 chunk 287 optimal weight: 50.0000 chunk 232 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 171 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28307 Z= 0.240 Angle : 0.623 8.238 38509 Z= 0.323 Chirality : 0.045 0.564 4442 Planarity : 0.005 0.059 4933 Dihedral : 5.445 23.148 3786 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.61 % 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: -1.78 (0.14), residues: 3462 helix: 0.45 (0.19), residues: 706 sheet: -1.53 (0.18), residues: 716 loop : -1.69 (0.13), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 3.738 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 outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.3982 time to fit residues: 61.4651 Evaluate side-chains 76 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 3.165 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3088 time to fit residues: 4.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 4.9990 chunk 302 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28307 Z= 0.170 Angle : 0.593 8.277 38509 Z= 0.302 Chirality : 0.045 0.575 4442 Planarity : 0.004 0.073 4933 Dihedral : 5.208 22.507 3786 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -1.65 (0.14), residues: 3462 helix: 0.57 (0.20), residues: 717 sheet: -1.38 (0.18), residues: 725 loop : -1.65 (0.13), residues: 2020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 3.267 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 outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3943 time to fit residues: 57.8896 Evaluate side-chains 75 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 30.0000 chunk 245 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 283 optimal weight: 40.0000 chunk 188 optimal weight: 40.0000 chunk 335 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 204 optimal weight: 0.0000 chunk 154 optimal weight: 9.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28307 Z= 0.177 Angle : 0.580 8.144 38509 Z= 0.297 Chirality : 0.045 0.515 4442 Planarity : 0.004 0.064 4933 Dihedral : 5.064 22.445 3786 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.54 (0.14), residues: 3462 helix: 0.79 (0.20), residues: 699 sheet: -1.33 (0.18), residues: 738 loop : -1.59 (0.13), residues: 2025 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 3.305 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 outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3870 time to fit residues: 57.0285 Evaluate side-chains 76 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.9990 chunk 133 optimal weight: 40.0000 chunk 200 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 213 optimal weight: 20.0000 chunk 228 optimal weight: 30.0000 chunk 165 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A1072 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28307 Z= 0.191 Angle : 0.594 12.647 38509 Z= 0.305 Chirality : 0.045 0.504 4442 Planarity : 0.004 0.065 4933 Dihedral : 5.048 22.053 3786 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -1.55 (0.14), residues: 3462 helix: 0.64 (0.20), residues: 716 sheet: -1.27 (0.18), residues: 718 loop : -1.59 (0.13), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.4298 time to fit residues: 62.1432 Evaluate side-chains 72 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 312 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28307 Z= 0.204 Angle : 0.603 9.308 38509 Z= 0.310 Chirality : 0.045 0.496 4442 Planarity : 0.004 0.065 4933 Dihedral : 5.078 25.786 3786 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -1.48 (0.14), residues: 3462 helix: 0.77 (0.20), residues: 704 sheet: -1.21 (0.18), residues: 723 loop : -1.57 (0.13), residues: 2035 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 3.260 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 outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.4011 time to fit residues: 56.9472 Evaluate side-chains 71 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 8.9990 chunk 330 optimal weight: 0.9990 chunk 201 optimal weight: 0.0770 chunk 156 optimal weight: 30.0000 chunk 229 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 319 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 28 optimal weight: 40.0000 chunk 213 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN A1072 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28307 Z= 0.187 Angle : 0.598 9.515 38509 Z= 0.306 Chirality : 0.045 0.480 4442 Planarity : 0.004 0.063 4933 Dihedral : 5.028 26.320 3786 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.43 (0.14), residues: 3462 helix: 0.82 (0.20), residues: 704 sheet: -1.20 (0.18), residues: 721 loop : -1.54 (0.13), residues: 2037 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 3.560 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 outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.4089 time to fit residues: 56.4392 Evaluate side-chains 71 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 254 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 218 ASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN ** C1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.025874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.017611 restraints weight = 632008.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.017757 restraints weight = 546472.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.017904 restraints weight = 495732.289| |-----------------------------------------------------------------------------| r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28307 Z= 0.206 Angle : 0.598 9.425 38509 Z= 0.308 Chirality : 0.045 0.484 4442 Planarity : 0.004 0.073 4933 Dihedral : 5.056 26.037 3786 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.65 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.43 (0.14), residues: 3462 helix: 0.82 (0.20), residues: 712 sheet: -1.30 (0.18), residues: 742 loop : -1.50 (0.14), residues: 2008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.37 seconds wall clock time: 69 minutes 39.02 seconds (4179.02 seconds total)