Starting phenix.real_space_refine on Thu Aug 8 22:31:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke8_22834/08_2024/7ke8_22834.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke8_22834/08_2024/7ke8_22834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke8_22834/08_2024/7ke8_22834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke8_22834/08_2024/7ke8_22834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke8_22834/08_2024/7ke8_22834.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke8_22834/08_2024/7ke8_22834.cif" } resolution = 3.26 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= -0.002 sd= 0.048 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 99 5.16 5 C 15282 2.51 5 N 3903 2.21 5 O 4710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23994 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7659 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 933} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7696 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 47, 'TRANS': 936} Chain breaks: 11 Chain: "C" Number of atoms: 7757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7757 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 48, 'TRANS': 943} Chain breaks: 10 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: 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: "F" 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: "G" 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: "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: 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.29, per 1000 atoms: 0.55 Number of scatterers: 23994 At special positions: 0 Unit cell: (141.772, 125.902, 171.396, 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 99 16.00 O 4710 8.00 N 3903 7.00 C 15282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 603 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 9.63 Conformation dependent library (CDL) restraints added in 4.5 seconds 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 49 sheets defined 27.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.595A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.027A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.251A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.819A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.883A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.646A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.501A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.567A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.528A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.734A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.736A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.973A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.102A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.627A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.656A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.682A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.863A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.727A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.629A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.531A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.637A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1143 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.020A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.537A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.501A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.754A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.537A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.501A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.677A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.678A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.505A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.014A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.273A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.607A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.654A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.266A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.916A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.743A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.948A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 removed outlier: 6.472A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.616A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.018A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.773A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.040A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.406A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.195A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.365A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.774A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.052A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.438A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.922A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.602A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.233A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.871A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.765A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.579A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.326A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.736A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.736A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.919A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.858A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 451 through 453 removed outlier: 4.360A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.582A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.90 Time building geometry restraints manager: 10.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6284 1.33 - 1.46: 4720 1.46 - 1.58: 13378 1.58 - 1.70: 0 1.70 - 1.83: 123 Bond restraints: 24505 Sorted by residual: bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.61e+01 bond pdb=" C5 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 24500 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.86: 373 104.86 - 112.45: 11624 112.45 - 120.04: 10752 120.04 - 127.63: 10447 127.63 - 135.21: 136 Bond angle restraints: 33332 Sorted by residual: angle pdb=" CA VAL A 635 " pdb=" CB VAL A 635 " pdb=" CG1 VAL A 635 " ideal model delta sigma weight residual 110.40 131.79 -21.39 1.70e+00 3.46e-01 1.58e+02 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.07 120.90 -11.83 1.52e+00 4.33e-01 6.05e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 119.30 -10.23 1.52e+00 4.33e-01 4.53e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 117.91 -8.95 1.49e+00 4.50e-01 3.61e+01 angle pdb=" C GLN C 321 " pdb=" CA GLN C 321 " pdb=" CB GLN C 321 " ideal model delta sigma weight residual 111.20 115.42 -4.22 7.10e-01 1.98e+00 3.54e+01 ... (remaining 33327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14282 17.94 - 35.88: 875 35.88 - 53.81: 156 53.81 - 71.75: 47 71.75 - 89.69: 33 Dihedral angle restraints: 15393 sinusoidal: 6788 harmonic: 8605 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.31 -89.69 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -171.71 85.71 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -167.57 81.57 1 1.00e+01 1.00e-02 8.19e+01 ... (remaining 15390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 3989 0.302 - 0.603: 9 0.603 - 0.905: 1 0.905 - 1.206: 0 1.206 - 1.508: 1 Chirality restraints: 4000 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.53e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.83e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.16e+01 ... (remaining 3997 not shown) Planarity restraints: 4258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.142 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN A 331 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.136 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN A 165 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.220 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.131 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" CG ASN B 331 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.220 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.171 2.00e-02 2.50e+03 ... (remaining 4255 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 12257 3.00 - 3.47: 23361 3.47 - 3.95: 39606 3.95 - 4.42: 44210 4.42 - 4.90: 74186 Nonbonded interactions: 193620 Sorted by model distance: nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.519 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.534 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.535 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.551 3.040 ... (remaining 193615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 623 or resid 635 through 1147 o \ r resid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 623 or resid 635 through 1147 o \ r resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 68.100 Find NCS groups from input model: 1.470 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.014 0.077 24505 Z= 0.881 Angle : 1.727 21.390 33332 Z= 1.148 Chirality : 0.101 1.508 4000 Planarity : 0.014 0.215 4210 Dihedral : 12.880 89.384 9731 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.30 % Favored : 93.56 % Rotamer: Outliers : 1.20 % Allowed : 2.67 % Favored : 96.13 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 2887 helix: -0.65 (0.17), residues: 679 sheet: 0.10 (0.22), residues: 519 loop : -0.86 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.022 TRP C 886 HIS 0.012 0.003 HIS B1048 PHE 0.079 0.012 PHE C 718 TYR 0.154 0.021 TYR A 451 ARG 0.009 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 266 time to evaluate : 2.726 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 168 PHE cc_start: 0.8334 (t80) cc_final: 0.7949 (t80) REVERT: A 571 ASP cc_start: 0.8199 (t0) cc_final: 0.7662 (t0) REVERT: A 603 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7873 (t0) REVERT: A 869 MET cc_start: 0.8879 (mtt) cc_final: 0.8650 (mtp) REVERT: B 218 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: B 360 ASN cc_start: 0.8928 (m-40) cc_final: 0.8446 (t0) REVERT: B 571 ASP cc_start: 0.7726 (t0) cc_final: 0.7387 (t0) REVERT: B 900 MET cc_start: 0.8438 (mtp) cc_final: 0.8227 (mtm) REVERT: B 994 ASP cc_start: 0.8338 (t70) cc_final: 0.8047 (t0) REVERT: C 62 VAL cc_start: 0.9305 (m) cc_final: 0.8985 (p) REVERT: C 105 ILE cc_start: 0.8205 (mt) cc_final: 0.7884 (tt) REVERT: C 110 LEU cc_start: 0.8730 (mp) cc_final: 0.8464 (mp) REVERT: C 366 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8683 (p) REVERT: C 394 ASN cc_start: 0.7352 (m-40) cc_final: 0.7086 (m-40) REVERT: C 424 LYS cc_start: 0.8533 (tptt) cc_final: 0.8150 (mttt) REVERT: C 436 TRP cc_start: 0.7664 (p90) cc_final: 0.7460 (p90) REVERT: C 633 TRP cc_start: 0.8830 (OUTLIER) cc_final: 0.6983 (t60) REVERT: C 697 MET cc_start: 0.8571 (ptm) cc_final: 0.8255 (ptm) REVERT: C 979 ASP cc_start: 0.8207 (m-30) cc_final: 0.8004 (m-30) outliers start: 31 outliers final: 9 residues processed: 293 average time/residue: 0.3969 time to fit residues: 176.4519 Evaluate side-chains 134 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 633 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 231 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 267 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN C 66 HIS C 360 ASN C 540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24505 Z= 0.196 Angle : 0.644 9.672 33332 Z= 0.342 Chirality : 0.046 0.331 4000 Planarity : 0.004 0.048 4210 Dihedral : 6.438 59.497 4491 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.59 % Allowed : 6.81 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2887 helix: 1.29 (0.20), residues: 666 sheet: 0.10 (0.19), residues: 619 loop : -0.64 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 353 HIS 0.004 0.001 HIS B1083 PHE 0.029 0.002 PHE C 168 TYR 0.019 0.002 TYR A1067 ARG 0.009 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 2.787 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 168 PHE cc_start: 0.8509 (t80) cc_final: 0.8248 (t80) REVERT: A 571 ASP cc_start: 0.8410 (t0) cc_final: 0.7808 (t0) REVERT: A 979 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7932 (t0) REVERT: B 360 ASN cc_start: 0.8840 (m-40) cc_final: 0.8487 (t0) REVERT: B 950 ASP cc_start: 0.8579 (t0) cc_final: 0.8219 (t0) REVERT: B 994 ASP cc_start: 0.8526 (t70) cc_final: 0.8284 (t0) REVERT: C 105 ILE cc_start: 0.8172 (mt) cc_final: 0.7769 (tt) REVERT: C 110 LEU cc_start: 0.8765 (mp) cc_final: 0.8563 (mp) REVERT: C 421 TYR cc_start: 0.4238 (OUTLIER) cc_final: 0.3243 (t80) REVERT: C 424 LYS cc_start: 0.8621 (tptt) cc_final: 0.8279 (mttt) REVERT: C 505 TYR cc_start: 0.8416 (m-80) cc_final: 0.7733 (t80) REVERT: C 633 TRP cc_start: 0.8839 (OUTLIER) cc_final: 0.6872 (t60) REVERT: C 697 MET cc_start: 0.8514 (ptm) cc_final: 0.8202 (ptm) outliers start: 41 outliers final: 14 residues processed: 179 average time/residue: 0.3319 time to fit residues: 96.7138 Evaluate side-chains 121 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 239 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 91 optimal weight: 0.0970 chunk 215 optimal weight: 6.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 207 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24505 Z= 0.351 Angle : 0.626 9.344 33332 Z= 0.328 Chirality : 0.046 0.222 4000 Planarity : 0.004 0.038 4210 Dihedral : 5.779 58.943 4475 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 1.70 % Allowed : 8.00 % Favored : 90.29 % 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: -0.13 (0.15), residues: 2887 helix: 1.38 (0.20), residues: 673 sheet: -0.11 (0.19), residues: 639 loop : -0.69 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 PHE 0.022 0.002 PHE C1089 TYR 0.024 0.002 TYR B1067 ARG 0.005 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7324 (m-90) cc_final: 0.6926 (m-90) REVERT: A 168 PHE cc_start: 0.8519 (t80) cc_final: 0.8262 (t80) REVERT: A 558 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8480 (mtmt) REVERT: A 979 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8108 (t0) REVERT: B 360 ASN cc_start: 0.8831 (m-40) cc_final: 0.8487 (t0) REVERT: B 950 ASP cc_start: 0.8579 (t0) cc_final: 0.8356 (t0) REVERT: C 105 ILE cc_start: 0.8232 (mt) cc_final: 0.7884 (tt) REVERT: C 400 PHE cc_start: 0.8620 (p90) cc_final: 0.8105 (p90) REVERT: C 421 TYR cc_start: 0.4354 (OUTLIER) cc_final: 0.3430 (t80) REVERT: C 424 LYS cc_start: 0.8673 (tptt) cc_final: 0.8274 (mttt) REVERT: C 505 TYR cc_start: 0.8492 (m-80) cc_final: 0.7747 (t80) REVERT: C 633 TRP cc_start: 0.8939 (OUTLIER) cc_final: 0.6919 (t60) REVERT: C 900 MET cc_start: 0.8345 (mtm) cc_final: 0.7957 (mtm) outliers start: 44 outliers final: 19 residues processed: 147 average time/residue: 0.3476 time to fit residues: 83.5280 Evaluate side-chains 122 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 901 GLN C1058 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 24505 Z= 0.185 Angle : 0.540 7.703 33332 Z= 0.282 Chirality : 0.043 0.254 4000 Planarity : 0.003 0.040 4210 Dihedral : 5.308 58.462 4475 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.33 % Rotamer: Outliers : 1.31 % Allowed : 8.78 % Favored : 89.91 % 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: 0.08 (0.15), residues: 2887 helix: 1.77 (0.20), residues: 666 sheet: -0.08 (0.19), residues: 641 loop : -0.62 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.002 0.001 HIS C 66 PHE 0.019 0.001 PHE A 238 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7147 (m-90) cc_final: 0.6874 (m-90) REVERT: A 168 PHE cc_start: 0.8545 (t80) cc_final: 0.8293 (t80) REVERT: A 269 TYR cc_start: 0.8118 (m-80) cc_final: 0.7735 (m-80) REVERT: A 756 TYR cc_start: 0.8833 (m-80) cc_final: 0.8588 (m-80) REVERT: A 979 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8100 (t0) REVERT: B 238 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6193 (p90) REVERT: B 360 ASN cc_start: 0.8795 (m-40) cc_final: 0.8480 (t0) REVERT: B 633 TRP cc_start: 0.4941 (OUTLIER) cc_final: 0.3588 (m-10) REVERT: C 105 ILE cc_start: 0.8200 (mt) cc_final: 0.7876 (tt) REVERT: C 390 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8722 (mp) REVERT: C 400 PHE cc_start: 0.8695 (p90) cc_final: 0.8128 (p90) REVERT: C 421 TYR cc_start: 0.4163 (OUTLIER) cc_final: 0.3258 (t80) REVERT: C 424 LYS cc_start: 0.8506 (tptt) cc_final: 0.8158 (mttp) REVERT: C 505 TYR cc_start: 0.8460 (m-80) cc_final: 0.7747 (t80) REVERT: C 633 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.6906 (t60) REVERT: C 697 MET cc_start: 0.8625 (ptm) cc_final: 0.8325 (ptm) REVERT: C 900 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7851 (mtm) outliers start: 34 outliers final: 16 residues processed: 148 average time/residue: 0.3697 time to fit residues: 86.4693 Evaluate side-chains 127 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 212 optimal weight: 0.0030 chunk 117 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24505 Z= 0.336 Angle : 0.580 8.153 33332 Z= 0.300 Chirality : 0.044 0.255 4000 Planarity : 0.004 0.039 4210 Dihedral : 5.240 57.687 4475 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 1.62 % Allowed : 9.36 % Favored : 89.02 % 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: -0.06 (0.15), residues: 2887 helix: 1.63 (0.20), residues: 672 sheet: -0.27 (0.18), residues: 674 loop : -0.66 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 PHE 0.019 0.002 PHE B 168 TYR 0.020 0.002 TYR B1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 2.941 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 104 TRP cc_start: 0.7345 (m-90) cc_final: 0.6950 (m-90) REVERT: A 168 PHE cc_start: 0.8543 (t80) cc_final: 0.8300 (t80) REVERT: A 558 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8396 (mtmt) REVERT: A 756 TYR cc_start: 0.8954 (m-80) cc_final: 0.8643 (m-80) REVERT: A 979 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 988 GLU cc_start: 0.7636 (mp0) cc_final: 0.7209 (pm20) REVERT: B 168 PHE cc_start: 0.8731 (t80) cc_final: 0.8442 (t80) REVERT: B 360 ASN cc_start: 0.8782 (m-40) cc_final: 0.8468 (t0) REVERT: B 633 TRP cc_start: 0.4886 (OUTLIER) cc_final: 0.3665 (m-10) REVERT: C 105 ILE cc_start: 0.8202 (mt) cc_final: 0.7898 (tt) REVERT: C 400 PHE cc_start: 0.8723 (p90) cc_final: 0.8136 (p90) REVERT: C 421 TYR cc_start: 0.4149 (OUTLIER) cc_final: 0.3289 (t80) REVERT: C 424 LYS cc_start: 0.8587 (tptt) cc_final: 0.8234 (mttt) REVERT: C 633 TRP cc_start: 0.8918 (OUTLIER) cc_final: 0.6880 (t60) REVERT: C 697 MET cc_start: 0.8637 (ptm) cc_final: 0.8359 (ptm) REVERT: C 900 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7970 (mtm) outliers start: 42 outliers final: 23 residues processed: 144 average time/residue: 0.3789 time to fit residues: 88.1569 Evaluate side-chains 131 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 285 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24505 Z= 0.217 Angle : 0.527 8.215 33332 Z= 0.273 Chirality : 0.043 0.240 4000 Planarity : 0.003 0.039 4210 Dihedral : 5.000 57.413 4474 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 1.43 % Allowed : 9.90 % Favored : 88.67 % 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: 0.05 (0.15), residues: 2887 helix: 1.80 (0.20), residues: 671 sheet: -0.18 (0.19), residues: 665 loop : -0.64 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.003 0.001 HIS C 245 PHE 0.027 0.001 PHE A 238 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 2.956 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 168 PHE cc_start: 0.8549 (t80) cc_final: 0.8317 (t80) REVERT: A 269 TYR cc_start: 0.7493 (m-80) cc_final: 0.7234 (m-10) REVERT: A 756 TYR cc_start: 0.8910 (m-80) cc_final: 0.8572 (m-80) REVERT: A 979 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8169 (t0) REVERT: A 988 GLU cc_start: 0.7708 (mp0) cc_final: 0.7240 (pm20) REVERT: B 238 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.5976 (p90) REVERT: B 360 ASN cc_start: 0.8820 (m-40) cc_final: 0.8524 (t0) REVERT: B 633 TRP cc_start: 0.4992 (OUTLIER) cc_final: 0.3776 (m-10) REVERT: B 661 GLU cc_start: 0.8393 (mp0) cc_final: 0.8130 (mp0) REVERT: C 105 ILE cc_start: 0.8192 (mt) cc_final: 0.7889 (tt) REVERT: C 323 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6395 (p) REVERT: C 400 PHE cc_start: 0.8713 (p90) cc_final: 0.8128 (p90) REVERT: C 421 TYR cc_start: 0.4243 (OUTLIER) cc_final: 0.3392 (t80) REVERT: C 424 LYS cc_start: 0.8583 (tptt) cc_final: 0.8251 (mttt) REVERT: C 633 TRP cc_start: 0.8899 (OUTLIER) cc_final: 0.6741 (t60) REVERT: C 697 MET cc_start: 0.8636 (ptm) cc_final: 0.8389 (ptm) REVERT: C 900 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7877 (mtm) outliers start: 37 outliers final: 19 residues processed: 145 average time/residue: 0.3606 time to fit residues: 85.1121 Evaluate side-chains 123 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 24505 Z= 0.300 Angle : 0.557 14.956 33332 Z= 0.288 Chirality : 0.044 0.246 4000 Planarity : 0.003 0.038 4210 Dihedral : 5.000 57.107 4474 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 1.70 % Allowed : 10.17 % Favored : 88.13 % 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: -0.03 (0.15), residues: 2887 helix: 1.72 (0.20), residues: 671 sheet: -0.27 (0.19), residues: 660 loop : -0.66 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 PHE 0.026 0.001 PHE B 238 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 2.691 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 168 PHE cc_start: 0.8554 (t80) cc_final: 0.8330 (t80) REVERT: A 221 SER cc_start: 0.8593 (t) cc_final: 0.8305 (p) REVERT: A 269 TYR cc_start: 0.7452 (m-80) cc_final: 0.7103 (m-10) REVERT: A 756 TYR cc_start: 0.8983 (m-80) cc_final: 0.8705 (m-80) REVERT: A 979 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 988 GLU cc_start: 0.7689 (mp0) cc_final: 0.7244 (pm20) REVERT: B 104 TRP cc_start: 0.7720 (m-90) cc_final: 0.7069 (m-90) REVERT: B 238 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6533 (p90) REVERT: B 360 ASN cc_start: 0.8816 (m-40) cc_final: 0.8545 (t0) REVERT: B 633 TRP cc_start: 0.4950 (OUTLIER) cc_final: 0.3865 (m-10) REVERT: B 661 GLU cc_start: 0.8459 (mp0) cc_final: 0.8214 (mp0) REVERT: C 105 ILE cc_start: 0.8197 (mt) cc_final: 0.7898 (tt) REVERT: C 323 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6417 (p) REVERT: C 400 PHE cc_start: 0.8668 (p90) cc_final: 0.8083 (p90) REVERT: C 421 TYR cc_start: 0.4202 (OUTLIER) cc_final: 0.3395 (t80) REVERT: C 424 LYS cc_start: 0.8608 (tptt) cc_final: 0.8256 (mttt) REVERT: C 633 TRP cc_start: 0.8948 (OUTLIER) cc_final: 0.6802 (t60) REVERT: C 697 MET cc_start: 0.8655 (ptm) cc_final: 0.8408 (ptm) REVERT: C 900 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7952 (mtm) outliers start: 44 outliers final: 28 residues processed: 145 average time/residue: 0.3780 time to fit residues: 87.7626 Evaluate side-chains 134 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 140 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 24505 Z= 0.246 Angle : 0.545 13.133 33332 Z= 0.281 Chirality : 0.043 0.247 4000 Planarity : 0.003 0.040 4210 Dihedral : 4.904 56.895 4474 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.62 % Allowed : 10.36 % Favored : 88.01 % 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: 0.02 (0.15), residues: 2887 helix: 1.73 (0.20), residues: 674 sheet: -0.22 (0.19), residues: 669 loop : -0.62 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS A 519 PHE 0.037 0.001 PHE B 168 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.6693 (t80) cc_final: 0.6459 (t80) REVERT: A 168 PHE cc_start: 0.8567 (t80) cc_final: 0.8346 (t80) REVERT: A 269 TYR cc_start: 0.7338 (m-80) cc_final: 0.6993 (m-10) REVERT: A 756 TYR cc_start: 0.8961 (m-80) cc_final: 0.8606 (m-80) REVERT: A 979 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8364 (t0) REVERT: A 988 GLU cc_start: 0.7727 (mp0) cc_final: 0.7245 (pm20) REVERT: B 238 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6324 (p90) REVERT: B 360 ASN cc_start: 0.8761 (m-40) cc_final: 0.8531 (t0) REVERT: B 633 TRP cc_start: 0.4910 (OUTLIER) cc_final: 0.3824 (m-10) REVERT: B 661 GLU cc_start: 0.8428 (mp0) cc_final: 0.8214 (mp0) REVERT: C 105 ILE cc_start: 0.8188 (mt) cc_final: 0.7891 (tt) REVERT: C 323 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6408 (p) REVERT: C 360 ASN cc_start: 0.8672 (p0) cc_final: 0.8442 (p0) REVERT: C 400 PHE cc_start: 0.8663 (p90) cc_final: 0.8061 (p90) REVERT: C 421 TYR cc_start: 0.4176 (OUTLIER) cc_final: 0.3289 (t80) REVERT: C 424 LYS cc_start: 0.8548 (tptt) cc_final: 0.8148 (mttt) REVERT: C 633 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.6799 (t60) REVERT: C 900 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7925 (mtm) outliers start: 42 outliers final: 29 residues processed: 147 average time/residue: 0.3415 time to fit residues: 81.4403 Evaluate side-chains 135 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.719 > 50: distance: 25 - 31: 9.743 distance: 31 - 32: 22.638 distance: 31 - 37: 27.209 distance: 32 - 33: 18.319 distance: 32 - 35: 23.569 distance: 33 - 34: 14.869 distance: 33 - 38: 37.406 distance: 35 - 36: 12.513 distance: 36 - 37: 13.230 distance: 38 - 39: 20.442 distance: 39 - 40: 37.679 distance: 39 - 42: 29.616 distance: 40 - 41: 5.223 distance: 40 - 44: 31.161 distance: 42 - 43: 9.608 distance: 44 - 45: 5.338 distance: 45 - 46: 21.303 distance: 45 - 48: 18.328 distance: 46 - 47: 21.360 distance: 46 - 53: 26.490 distance: 48 - 49: 21.367 distance: 49 - 50: 22.276 distance: 50 - 51: 6.180 distance: 51 - 52: 23.099 distance: 53 - 54: 40.975 distance: 53 - 59: 10.397 distance: 54 - 55: 58.959 distance: 55 - 56: 18.642 distance: 55 - 60: 21.461 distance: 57 - 58: 36.767 distance: 58 - 59: 4.975 distance: 60 - 61: 16.437 distance: 61 - 62: 9.811 distance: 61 - 64: 11.632 distance: 62 - 63: 5.881 distance: 62 - 66: 8.456 distance: 66 - 67: 35.320 distance: 67 - 68: 34.820 distance: 67 - 70: 16.056 distance: 68 - 69: 6.184 distance: 68 - 75: 14.129 distance: 70 - 71: 29.149 distance: 72 - 73: 7.706 distance: 73 - 74: 11.694 distance: 75 - 76: 24.231 distance: 76 - 77: 13.980 distance: 76 - 79: 14.016 distance: 77 - 78: 8.827 distance: 77 - 86: 43.807 distance: 79 - 80: 21.199 distance: 80 - 81: 8.046 distance: 81 - 82: 12.652 distance: 82 - 83: 7.904 distance: 83 - 84: 8.484 distance: 83 - 85: 14.589 distance: 86 - 87: 20.364 distance: 87 - 88: 25.122 distance: 87 - 90: 6.853 distance: 88 - 89: 14.514 distance: 88 - 92: 4.154 distance: 89 - 120: 34.553 distance: 92 - 93: 3.072 distance: 93 - 94: 11.309 distance: 93 - 96: 3.889 distance: 94 - 95: 5.203 distance: 94 - 103: 7.532 distance: 95 - 128: 34.214 distance: 96 - 97: 18.937 distance: 97 - 98: 9.595 distance: 97 - 99: 11.498 distance: 98 - 100: 14.527 distance: 99 - 101: 19.518 distance: 103 - 104: 10.541 distance: 104 - 105: 14.726 distance: 104 - 107: 20.359 distance: 105 - 106: 19.488 distance: 105 - 111: 24.094 distance: 106 - 136: 13.738 distance: 107 - 108: 4.498 distance: 107 - 109: 32.461 distance: 108 - 110: 5.357