Starting phenix.real_space_refine on Tue Jun 24 04:55:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymy_33947/06_2025/7ymy_33947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymy_33947/06_2025/7ymy_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/cci-nas-00/data/ceres_data/7ymy_33947/06_2025/7ymy_33947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymy_33947/06_2025/7ymy_33947.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymy_33947/06_2025/7ymy_33947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymy_33947/06_2025/7ymy_33947.cif" } 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. Time to flip 5 residue(s): 0.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 21 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 dihedrals: 15 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.53, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 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: 7.57 Conformation dependent library (CDL) restraints added in 3.5 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: 4.36 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: 12.91 Time building geometry restraints manager: 8.88 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: 0.00 - 2.48: 37413 2.48 - 4.95: 890 4.95 - 7.43: 166 7.43 - 9.91: 34 9.91 - 12.38: 6 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 - 24.66: 16337 24.66 - 49.32: 910 49.32 - 73.97: 138 73.97 - 98.63: 71 98.63 - 123.29: 22 Dihedral angle restraints: 17478 sinusoidal: 7287 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 17475 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 3.040 nonbonded pdb=" OG SER C 643 " pdb=" OD1 ASP C 645 " model vdw 2.205 3.040 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 397 " pdb=" O PRO A 531 " model vdw 2.212 3.040 nonbonded pdb=" NE2 GLN B 427 " pdb=" O ASN B 475 " model vdw 2.213 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.920 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: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 66.930 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.770 ------------------------------------------------------------------------------- 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 28401 Z= 0.313 Angle : 1.012 22.537 38743 Z= 0.526 Chirality : 0.064 1.066 4442 Planarity : 0.007 0.106 4933 Dihedral : 16.635 123.289 10824 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B1184 HIS 0.009 0.001 HIS A 167 PHE 0.056 0.003 PHE C 266 TYR 0.038 0.002 TYR B 241 ARG 0.010 0.001 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 28) link_NAG-ASN : angle 6.26268 ( 84) link_ALPHA1-6 : bond 0.00285 ( 2) link_ALPHA1-6 : angle 1.88249 ( 6) link_BETA1-4 : bond 0.01328 ( 13) link_BETA1-4 : angle 3.94593 ( 39) link_ALPHA1-3 : bond 0.00424 ( 3) link_ALPHA1-3 : angle 2.06485 ( 9) hydrogen bonds : bond 0.14397 ( 1015) hydrogen bonds : angle 7.70331 ( 2736) SS BOND : bond 0.00373 ( 48) SS BOND : angle 1.78617 ( 96) covalent geometry : bond 0.00570 (28307) covalent geometry : angle 0.95899 (38509) *********************** 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 to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.9664 (pp) cc_final: 0.9439 (tt) REVERT: A 240 MET cc_start: 0.7916 (mtm) cc_final: 0.7019 (mmm) REVERT: A 277 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8038 (p0) REVERT: A 757 MET cc_start: 0.8331 (tpp) cc_final: 0.7930 (tpp) REVERT: A 1062 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9270 (mp0) REVERT: B 268 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7878 (t) REVERT: B 273 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9258 (tp) REVERT: B 563 MET cc_start: 0.7525 (mmp) cc_final: 0.5641 (mmp) REVERT: B 569 MET cc_start: 0.9457 (mpp) cc_final: 0.8999 (mmp) REVERT: B 590 PHE cc_start: 0.8596 (m-10) cc_final: 0.8142 (t80) REVERT: B 757 MET cc_start: 0.8313 (tpp) cc_final: 0.7162 (mtt) REVERT: C 84 MET cc_start: 0.8936 (tmm) cc_final: 0.8642 (tmm) REVERT: C 161 MET cc_start: 0.9491 (ppp) cc_final: 0.9192 (ppp) REVERT: C 167 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7848 (t70) REVERT: C 875 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8951 (tm-30) outliers start: 15 outliers final: 6 residues processed: 147 average time/residue: 0.4021 time to fit residues: 95.2898 Evaluate side-chains 98 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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: 30.0000 chunk 263 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 177 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 165 optimal weight: 9.9990 chunk 203 optimal weight: 50.0000 chunk 316 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN A1145 ASN B 521 ASN B 812 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN C 836 HIS C1072 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.029208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.020645 restraints weight = 606161.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.020844 restraints weight = 502648.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.021087 restraints weight = 443899.469| |-----------------------------------------------------------------------------| r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28401 Z= 0.176 Angle : 0.702 18.545 38743 Z= 0.349 Chirality : 0.047 0.686 4442 Planarity : 0.005 0.063 4933 Dihedral : 11.386 118.158 4734 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % 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: -1.76 (0.14), residues: 3462 helix: 0.19 (0.19), residues: 707 sheet: -1.28 (0.18), residues: 740 loop : -1.66 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.011 0.001 HIS C 167 PHE 0.036 0.002 PHE C 165 TYR 0.017 0.002 TYR B 314 ARG 0.006 0.001 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00925 ( 28) link_NAG-ASN : angle 4.72116 ( 84) link_ALPHA1-6 : bond 0.00442 ( 2) link_ALPHA1-6 : angle 2.18685 ( 6) link_BETA1-4 : bond 0.00830 ( 13) link_BETA1-4 : angle 2.64812 ( 39) link_ALPHA1-3 : bond 0.01130 ( 3) link_ALPHA1-3 : angle 4.85710 ( 9) hydrogen bonds : bond 0.04344 ( 1015) hydrogen bonds : angle 6.65139 ( 2736) SS BOND : bond 0.00450 ( 48) SS BOND : angle 1.20085 ( 96) covalent geometry : bond 0.00354 (28307) covalent geometry : angle 0.65629 (38509) *********************** 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 105 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8727 (m-80) cc_final: 0.8319 (m-80) REVERT: A 171 LEU cc_start: 0.9678 (mp) cc_final: 0.9448 (pp) REVERT: A 757 MET cc_start: 0.9507 (tpp) cc_final: 0.9076 (tpp) REVERT: B 569 MET cc_start: 0.9492 (mpp) cc_final: 0.9127 (mmp) REVERT: B 824 TYR cc_start: 0.9388 (m-10) cc_final: 0.9115 (m-80) REVERT: C 84 MET cc_start: 0.9359 (tmm) cc_final: 0.9146 (tmm) REVERT: C 161 MET cc_start: 0.8939 (ppp) cc_final: 0.8654 (ppp) REVERT: C 278 MET cc_start: 0.8788 (tpp) cc_final: 0.8519 (tpp) REVERT: C 824 TYR cc_start: 0.9566 (m-10) cc_final: 0.9207 (m-80) REVERT: C 939 MET cc_start: 0.8526 (tpt) cc_final: 0.8318 (tpt) REVERT: C 943 MET cc_start: 0.9673 (ttp) cc_final: 0.9471 (ttp) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.3753 time to fit residues: 67.7879 Evaluate side-chains 81 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 257 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 278 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 293 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 300 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN C 681 HIS C 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.029186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.020657 restraints weight = 602442.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.020869 restraints weight = 492973.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.021124 restraints weight = 433115.395| |-----------------------------------------------------------------------------| r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28401 Z= 0.143 Angle : 0.662 18.749 38743 Z= 0.325 Chirality : 0.047 0.671 4442 Planarity : 0.005 0.069 4933 Dihedral : 10.620 118.903 4734 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3462 helix: 0.36 (0.19), residues: 708 sheet: -1.28 (0.18), residues: 732 loop : -1.61 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 960 HIS 0.011 0.001 HIS C 167 PHE 0.015 0.001 PHE C 967 TYR 0.023 0.001 TYR C 184 ARG 0.005 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 28) link_NAG-ASN : angle 4.63708 ( 84) link_ALPHA1-6 : bond 0.00622 ( 2) link_ALPHA1-6 : angle 1.85354 ( 6) link_BETA1-4 : bond 0.00677 ( 13) link_BETA1-4 : angle 2.48974 ( 39) link_ALPHA1-3 : bond 0.01176 ( 3) link_ALPHA1-3 : angle 3.52488 ( 9) hydrogen bonds : bond 0.04018 ( 1015) hydrogen bonds : angle 6.46944 ( 2736) SS BOND : bond 0.00463 ( 48) SS BOND : angle 1.18296 ( 96) covalent geometry : bond 0.00297 (28307) covalent geometry : angle 0.61688 (38509) *********************** 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 99 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 2.886 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: A 757 MET cc_start: 0.9486 (tpp) cc_final: 0.9066 (tpp) REVERT: B 569 MET cc_start: 0.9509 (mpp) cc_final: 0.9142 (mmp) REVERT: B 824 TYR cc_start: 0.9260 (m-10) cc_final: 0.8984 (m-80) REVERT: B 939 MET cc_start: 0.9638 (mpp) cc_final: 0.8989 (mtp) REVERT: C 824 TYR cc_start: 0.9488 (m-10) cc_final: 0.9085 (m-80) REVERT: C 939 MET cc_start: 0.8688 (tpt) cc_final: 0.8381 (tpt) REVERT: C 943 MET cc_start: 0.9667 (ttp) cc_final: 0.9410 (ttp) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.4137 time to fit residues: 69.2921 Evaluate side-chains 81 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 304 optimal weight: 9.9990 chunk 257 optimal weight: 0.0060 chunk 220 optimal weight: 20.0000 chunk 157 optimal weight: 50.0000 chunk 290 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 285 optimal weight: 50.0000 chunk 105 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.029073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.020517 restraints weight = 606656.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.020739 restraints weight = 494435.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.021003 restraints weight = 432500.950| |-----------------------------------------------------------------------------| r_work (final): 0.2335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28401 Z= 0.134 Angle : 0.649 18.588 38743 Z= 0.317 Chirality : 0.047 0.714 4442 Planarity : 0.005 0.060 4933 Dihedral : 9.850 118.516 4734 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: -1.56 (0.14), residues: 3462 helix: 0.61 (0.20), residues: 688 sheet: -1.31 (0.18), residues: 747 loop : -1.54 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 253 HIS 0.003 0.001 HIS C 167 PHE 0.016 0.001 PHE C 967 TYR 0.028 0.001 TYR B 241 ARG 0.008 0.000 ARG B 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 28) link_NAG-ASN : angle 4.49367 ( 84) link_ALPHA1-6 : bond 0.00690 ( 2) link_ALPHA1-6 : angle 1.54644 ( 6) link_BETA1-4 : bond 0.00679 ( 13) link_BETA1-4 : angle 2.38478 ( 39) link_ALPHA1-3 : bond 0.01060 ( 3) link_ALPHA1-3 : angle 3.66867 ( 9) hydrogen bonds : bond 0.03812 ( 1015) hydrogen bonds : angle 6.37631 ( 2736) SS BOND : bond 0.00759 ( 48) SS BOND : angle 1.18413 ( 96) covalent geometry : bond 0.00281 (28307) covalent geometry : angle 0.60611 (38509) *********************** 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 93 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.903 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: A 147 PHE cc_start: 0.8655 (m-80) cc_final: 0.8291 (m-80) REVERT: A 171 LEU cc_start: 0.9597 (mp) cc_final: 0.9348 (pp) REVERT: A 757 MET cc_start: 0.9491 (tpp) cc_final: 0.9074 (tpp) REVERT: B 569 MET cc_start: 0.9496 (mpp) cc_final: 0.9128 (mmp) REVERT: B 939 MET cc_start: 0.9639 (mpp) cc_final: 0.8997 (mtp) REVERT: C 939 MET cc_start: 0.8673 (tpt) cc_final: 0.8344 (tpt) REVERT: C 943 MET cc_start: 0.9693 (ttp) cc_final: 0.9493 (ttp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4028 time to fit residues: 64.9105 Evaluate side-chains 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 225 optimal weight: 8.9990 chunk 234 optimal weight: 20.0000 chunk 204 optimal weight: 0.0370 chunk 261 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 299 optimal weight: 30.0000 chunk 271 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 259 optimal weight: 0.4980 overall best weight: 4.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 466 GLN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.028811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.020345 restraints weight = 601191.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.020603 restraints weight = 490069.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.020767 restraints weight = 430065.167| |-----------------------------------------------------------------------------| r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28401 Z= 0.134 Angle : 0.637 18.091 38743 Z= 0.311 Chirality : 0.047 0.680 4442 Planarity : 0.004 0.059 4933 Dihedral : 9.144 116.833 4734 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % 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: -1.46 (0.14), residues: 3462 helix: 0.73 (0.20), residues: 693 sheet: -1.25 (0.18), residues: 725 loop : -1.51 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 253 HIS 0.005 0.001 HIS A1122 PHE 0.016 0.001 PHE C 266 TYR 0.018 0.001 TYR B 241 ARG 0.004 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 28) link_NAG-ASN : angle 4.47690 ( 84) link_ALPHA1-6 : bond 0.00816 ( 2) link_ALPHA1-6 : angle 1.95552 ( 6) link_BETA1-4 : bond 0.00712 ( 13) link_BETA1-4 : angle 2.38028 ( 39) link_ALPHA1-3 : bond 0.01248 ( 3) link_ALPHA1-3 : angle 3.59824 ( 9) hydrogen bonds : bond 0.03721 ( 1015) hydrogen bonds : angle 6.26429 ( 2736) SS BOND : bond 0.00290 ( 48) SS BOND : angle 1.18115 ( 96) covalent geometry : bond 0.00280 (28307) covalent geometry : angle 0.59321 (38509) *********************** 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 93 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 6.186 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: A 147 PHE cc_start: 0.8640 (m-80) cc_final: 0.8291 (m-80) REVERT: A 171 LEU cc_start: 0.9603 (mp) cc_final: 0.9363 (pp) REVERT: A 757 MET cc_start: 0.9490 (tpp) cc_final: 0.9091 (tpp) REVERT: B 569 MET cc_start: 0.9461 (mpp) cc_final: 0.9121 (mmp) REVERT: B 757 MET cc_start: 0.9432 (tpp) cc_final: 0.8199 (mtt) REVERT: C 939 MET cc_start: 0.8633 (tpt) cc_final: 0.7954 (tpt) REVERT: C 943 MET cc_start: 0.9683 (ttp) cc_final: 0.9450 (mtm) outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.5559 time to fit residues: 92.3201 Evaluate side-chains 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 202 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 198 optimal weight: 50.0000 chunk 243 optimal weight: 30.0000 chunk 226 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 297 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.028548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.020068 restraints weight = 608218.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.020336 restraints weight = 498444.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.020585 restraints weight = 428907.887| |-----------------------------------------------------------------------------| r_work (final): 0.2324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28401 Z= 0.140 Angle : 0.637 17.957 38743 Z= 0.312 Chirality : 0.047 0.681 4442 Planarity : 0.004 0.061 4933 Dihedral : 8.798 113.431 4734 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3462 helix: 0.78 (0.20), residues: 692 sheet: -1.23 (0.18), residues: 715 loop : -1.49 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 253 HIS 0.005 0.001 HIS C 167 PHE 0.014 0.001 PHE C 266 TYR 0.022 0.001 TYR C 184 ARG 0.007 0.000 ARG C 652 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 28) link_NAG-ASN : angle 4.30728 ( 84) link_ALPHA1-6 : bond 0.00760 ( 2) link_ALPHA1-6 : angle 1.40403 ( 6) link_BETA1-4 : bond 0.00684 ( 13) link_BETA1-4 : angle 2.29795 ( 39) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 3.57478 ( 9) hydrogen bonds : bond 0.03703 ( 1015) hydrogen bonds : angle 6.26601 ( 2736) SS BOND : bond 0.00372 ( 48) SS BOND : angle 1.21235 ( 96) covalent geometry : bond 0.00292 (28307) covalent geometry : angle 0.59594 (38509) *********************** 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 90 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.948 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: A 147 PHE cc_start: 0.8597 (m-80) cc_final: 0.8248 (m-80) REVERT: A 171 LEU cc_start: 0.9600 (mp) cc_final: 0.9343 (pp) REVERT: A 757 MET cc_start: 0.9489 (tpp) cc_final: 0.9094 (tpp) REVERT: B 569 MET cc_start: 0.9450 (mpp) cc_final: 0.9139 (mmp) REVERT: B 939 MET cc_start: 0.9475 (pmm) cc_final: 0.9238 (pmm) REVERT: C 939 MET cc_start: 0.8600 (tpt) cc_final: 0.8050 (tpt) REVERT: C 943 MET cc_start: 0.9694 (ttp) cc_final: 0.9438 (mtm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4193 time to fit residues: 64.8221 Evaluate side-chains 77 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 152 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 306 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 125 optimal weight: 40.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A1016 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 98 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 ASN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.026613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.018937 restraints weight = 635627.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.019203 restraints weight = 517774.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.019364 restraints weight = 453676.356| |-----------------------------------------------------------------------------| r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28401 Z= 0.195 Angle : 0.686 17.613 38743 Z= 0.343 Chirality : 0.047 0.700 4442 Planarity : 0.005 0.061 4933 Dihedral : 8.732 112.660 4734 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -1.49 (0.14), residues: 3462 helix: 0.76 (0.19), residues: 690 sheet: -1.33 (0.18), residues: 726 loop : -1.51 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 253 HIS 0.004 0.001 HIS A1122 PHE 0.022 0.002 PHE B 281 TYR 0.016 0.002 TYR C 184 ARG 0.012 0.001 ARG C 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 28) link_NAG-ASN : angle 4.31438 ( 84) link_ALPHA1-6 : bond 0.00688 ( 2) link_ALPHA1-6 : angle 1.57849 ( 6) link_BETA1-4 : bond 0.00818 ( 13) link_BETA1-4 : angle 2.31603 ( 39) link_ALPHA1-3 : bond 0.00955 ( 3) link_ALPHA1-3 : angle 4.04053 ( 9) hydrogen bonds : bond 0.04164 ( 1015) hydrogen bonds : angle 6.55378 ( 2736) SS BOND : bond 0.00384 ( 48) SS BOND : angle 1.41487 ( 96) covalent geometry : bond 0.00400 (28307) covalent geometry : angle 0.64717 (38509) *********************** 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 86 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 3.708 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: A 147 PHE cc_start: 0.8676 (m-80) cc_final: 0.8320 (m-80) REVERT: A 171 LEU cc_start: 0.9574 (mp) cc_final: 0.9270 (pp) REVERT: A 757 MET cc_start: 0.9490 (tpp) cc_final: 0.9146 (tpp) REVERT: B 569 MET cc_start: 0.9448 (mpp) cc_final: 0.9085 (mmp) REVERT: B 757 MET cc_start: 0.9416 (tpp) cc_final: 0.8334 (mtt) REVERT: C 939 MET cc_start: 0.8728 (tpt) cc_final: 0.8504 (tpt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.4528 time to fit residues: 68.0888 Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 39 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 299 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 212 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 98 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.028051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.019674 restraints weight = 611239.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.019946 restraints weight = 495925.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.020234 restraints weight = 428849.136| |-----------------------------------------------------------------------------| r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28401 Z= 0.126 Angle : 0.656 17.454 38743 Z= 0.318 Chirality : 0.047 0.684 4442 Planarity : 0.005 0.087 4933 Dihedral : 8.606 113.108 4734 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -1.39 (0.14), residues: 3462 helix: 0.90 (0.20), residues: 689 sheet: -1.25 (0.18), residues: 722 loop : -1.47 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 253 HIS 0.007 0.001 HIS A 167 PHE 0.026 0.001 PHE C 467 TYR 0.023 0.001 TYR B 314 ARG 0.004 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 28) link_NAG-ASN : angle 4.19142 ( 84) link_ALPHA1-6 : bond 0.00705 ( 2) link_ALPHA1-6 : angle 1.50232 ( 6) link_BETA1-4 : bond 0.00695 ( 13) link_BETA1-4 : angle 2.14383 ( 39) link_ALPHA1-3 : bond 0.01008 ( 3) link_ALPHA1-3 : angle 3.37272 ( 9) hydrogen bonds : bond 0.03624 ( 1015) hydrogen bonds : angle 6.30565 ( 2736) SS BOND : bond 0.00367 ( 48) SS BOND : angle 1.49118 ( 96) covalent geometry : bond 0.00276 (28307) covalent geometry : angle 0.61773 (38509) *********************** 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 85 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8595 (m-80) cc_final: 0.8289 (m-80) REVERT: A 171 LEU cc_start: 0.9576 (mp) cc_final: 0.9374 (pp) REVERT: A 757 MET cc_start: 0.9482 (tpp) cc_final: 0.9112 (tpp) REVERT: B 569 MET cc_start: 0.9407 (mpp) cc_final: 0.9109 (mmp) REVERT: B 939 MET cc_start: 0.9531 (pmm) cc_final: 0.9317 (pmm) REVERT: C 939 MET cc_start: 0.8673 (tpt) cc_final: 0.8418 (tpt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3600 time to fit residues: 52.8341 Evaluate side-chains 72 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 323 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.027195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.019031 restraints weight = 622489.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.019275 restraints weight = 510252.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.019446 restraints weight = 444337.434| |-----------------------------------------------------------------------------| r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28401 Z= 0.178 Angle : 0.675 17.097 38743 Z= 0.336 Chirality : 0.047 0.712 4442 Planarity : 0.005 0.069 4933 Dihedral : 8.507 111.572 4734 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.39 (0.14), residues: 3462 helix: 0.85 (0.20), residues: 695 sheet: -1.24 (0.18), residues: 713 loop : -1.46 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 253 HIS 0.006 0.001 HIS B 681 PHE 0.032 0.002 PHE C 467 TYR 0.019 0.002 TYR B 314 ARG 0.005 0.001 ARG C 629 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 28) link_NAG-ASN : angle 4.20827 ( 84) link_ALPHA1-6 : bond 0.00657 ( 2) link_ALPHA1-6 : angle 1.54808 ( 6) link_BETA1-4 : bond 0.00714 ( 13) link_BETA1-4 : angle 2.24973 ( 39) link_ALPHA1-3 : bond 0.00802 ( 3) link_ALPHA1-3 : angle 3.71061 ( 9) hydrogen bonds : bond 0.04011 ( 1015) hydrogen bonds : angle 6.51756 ( 2736) SS BOND : bond 0.00414 ( 48) SS BOND : angle 1.60734 ( 96) covalent geometry : bond 0.00370 (28307) covalent geometry : angle 0.63636 (38509) *********************** 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 to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 3.327 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: A 147 PHE cc_start: 0.8559 (m-80) cc_final: 0.8118 (m-80) REVERT: A 171 LEU cc_start: 0.9558 (mp) cc_final: 0.9221 (pp) REVERT: A 757 MET cc_start: 0.8742 (tpp) cc_final: 0.8484 (tpp) REVERT: A 1008 MET cc_start: 0.9630 (ppp) cc_final: 0.9306 (ttt) REVERT: B 569 MET cc_start: 0.9435 (mpp) cc_final: 0.9109 (mmp) REVERT: B 757 MET cc_start: 0.9192 (tpp) cc_final: 0.8173 (mtt) REVERT: C 939 MET cc_start: 0.8515 (tpt) cc_final: 0.8103 (tpt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3854 time to fit residues: 54.3459 Evaluate side-chains 69 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 191 optimal weight: 0.9990 chunk 120 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 13 optimal weight: 50.0000 chunk 258 optimal weight: 30.0000 chunk 192 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 183 optimal weight: 40.0000 chunk 263 optimal weight: 4.9990 overall best weight: 6.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.019002 restraints weight = 620807.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.019212 restraints weight = 503123.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.019496 restraints weight = 438170.133| |-----------------------------------------------------------------------------| r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28401 Z= 0.163 Angle : 0.671 17.189 38743 Z= 0.332 Chirality : 0.047 0.711 4442 Planarity : 0.004 0.064 4933 Dihedral : 8.493 111.999 4734 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -1.41 (0.14), residues: 3462 helix: 0.77 (0.20), residues: 704 sheet: -1.26 (0.18), residues: 720 loop : -1.45 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 253 HIS 0.004 0.001 HIS A1122 PHE 0.018 0.002 PHE C 467 TYR 0.018 0.001 TYR A 270 ARG 0.005 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 28) link_NAG-ASN : angle 4.18795 ( 84) link_ALPHA1-6 : bond 0.00613 ( 2) link_ALPHA1-6 : angle 1.58559 ( 6) link_BETA1-4 : bond 0.00740 ( 13) link_BETA1-4 : angle 2.17467 ( 39) link_ALPHA1-3 : bond 0.00824 ( 3) link_ALPHA1-3 : angle 3.55696 ( 9) hydrogen bonds : bond 0.03898 ( 1015) hydrogen bonds : angle 6.52954 ( 2736) SS BOND : bond 0.00413 ( 48) SS BOND : angle 1.72319 ( 96) covalent geometry : bond 0.00340 (28307) covalent geometry : angle 0.63184 (38509) ********************** 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 82 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8545 (m-80) cc_final: 0.8113 (m-80) REVERT: A 171 LEU cc_start: 0.9557 (mp) cc_final: 0.9228 (pp) REVERT: A 757 MET cc_start: 0.8680 (tpp) cc_final: 0.8399 (tpp) REVERT: B 569 MET cc_start: 0.9414 (mpp) cc_final: 0.9116 (mmp) REVERT: B 757 MET cc_start: 0.9167 (tpp) cc_final: 0.8186 (mtt) REVERT: B 906 MET cc_start: 0.9326 (tpt) cc_final: 0.8969 (tpt) REVERT: C 939 MET cc_start: 0.8562 (tpt) cc_final: 0.8090 (tpt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3940 time to fit residues: 55.1541 Evaluate side-chains 70 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 66 optimal weight: 40.0000 chunk 203 optimal weight: 8.9990 chunk 229 optimal weight: 0.1980 chunk 307 optimal weight: 30.0000 chunk 217 optimal weight: 7.9990 chunk 181 optimal weight: 30.0000 chunk 150 optimal weight: 0.0970 chunk 147 optimal weight: 20.0000 chunk 346 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 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 974 GLN C 98 GLN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.027851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.019540 restraints weight = 610055.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.019857 restraints weight = 490872.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.020087 restraints weight = 422297.409| |-----------------------------------------------------------------------------| r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28401 Z= 0.118 Angle : 0.660 16.789 38743 Z= 0.321 Chirality : 0.047 0.668 4442 Planarity : 0.004 0.056 4933 Dihedral : 8.302 110.413 4734 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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: -1.29 (0.14), residues: 3462 helix: 0.94 (0.20), residues: 695 sheet: -1.18 (0.18), residues: 737 loop : -1.40 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 253 HIS 0.005 0.001 HIS B1138 PHE 0.022 0.001 PHE C 467 TYR 0.016 0.001 TYR B 241 ARG 0.017 0.001 ARG C 401 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 28) link_NAG-ASN : angle 4.08273 ( 84) link_ALPHA1-6 : bond 0.00735 ( 2) link_ALPHA1-6 : angle 1.52636 ( 6) link_BETA1-4 : bond 0.00708 ( 13) link_BETA1-4 : angle 2.09090 ( 39) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 3.09338 ( 9) hydrogen bonds : bond 0.03550 ( 1015) hydrogen bonds : angle 6.24954 ( 2736) SS BOND : bond 0.00312 ( 48) SS BOND : angle 1.61630 ( 96) covalent geometry : bond 0.00264 (28307) covalent geometry : angle 0.62305 (38509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7996.16 seconds wall clock time: 146 minutes 11.30 seconds (8771.30 seconds total)