Starting phenix.real_space_refine on Sun Mar 10 14:46:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/03_2024/7xu1_33455_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/03_2024/7xu1_33455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/03_2024/7xu1_33455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/03_2024/7xu1_33455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/03_2024/7xu1_33455_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/03_2024/7xu1_33455_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17134 2.51 5 N 4401 2.21 5 O 5256 1.98 5 H 25165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52082 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 17102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17102 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "A" Number of atoms: 16846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 16846 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 50, 'TRANS': 1041} Chain breaks: 4 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: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 211 Unusual residues: {'BLA': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 265 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 17.20, per 1000 atoms: 0.33 Number of scatterers: 52082 At special positions: 0 Unit cell: (140.052, 152.784, 171.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5256 8.00 N 4401 7.00 C 17134 6.00 H 25165 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.03 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=2.06 Simple disulfide: pdb=" SG CYS C 427 " - pdb=" SG CYS A 987 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS A 427 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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-ASN " NAG A1802 " - " ASN A 331 " " NAG A1803 " - " ASN A 603 " " NAG A1804 " - " ASN A 616 " " NAG A1805 " - " ASN A 657 " " NAG A1806 " - " ASN A 709 " " NAG A1807 " - " ASN A1074 " " NAG A1808 " - " ASN A1098 " " NAG A1809 " - " ASN A 165 " " NAG A1810 " - " ASN A 282 " " NAG A1811 " - " ASN A 343 " " NAG A1813 " - " ASN A 17 " " NAG A1814 " - " ASN A 61 " " NAG A1815 " - " ASN A 149 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 343 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN C 234 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN C 801 " " NAG G 1 " - " ASN C1134 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 122 " Time building additional restraints: 30.56 Conformation dependent library (CDL) restraints added in 3.8 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB VAL B 70 " Number of C-beta restraints generated: 6188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 43 sheets defined 20.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 367 through 370 removed outlier: 3.663A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.265A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.669A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 631 through 636' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 754 through 782 removed outlier: 4.710A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 761 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 764 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 772 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU C 780 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 782 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 837 through 842 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.958A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1031 removed outlier: 3.680A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.228A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.570A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.590A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.594A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.735A pdb=" N TYR B 917 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 938 Processing helix chain 'B' and resid 943 through 967 removed outlier: 4.406A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 949 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 954 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 4.052A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.662A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.487A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 944 through 967 removed outlier: 3.828A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 3.715A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.115A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.902A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.565A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= F, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.033A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.511A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 691 through 696 removed outlier: 5.920A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= K, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.000A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= M, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id= O, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.473A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 48 through 55 Processing sheet with id= Q, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= S, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.066A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= W, first strand: chain 'B' and resid 539 through 543 Processing sheet with id= X, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.203A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 691 through 696 removed outlier: 3.592A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 718 through 728 Processing sheet with id= AA, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AB, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id= AC, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 6.915A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.540A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= AG, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.994A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.418A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.865A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'A' and resid 551 through 554 Processing sheet with id= AL, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.294A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= AN, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.857A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= AP, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= AQ, first strand: chain 'A' and resid 1094 through 1097 877 hydrogen bonds defined for protein. 2262 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: 18.52 Time building geometry restraints manager: 32.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 25159 1.05 - 1.27: 4340 1.27 - 1.48: 11425 1.48 - 1.69: 11606 1.69 - 1.91: 156 Bond restraints: 52686 Sorted by residual: bond pdb=" C1C BLA B1313 " pdb=" NC BLA B1313 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C4C BLA C1313 " pdb=" NC BLA C1313 " ideal model delta sigma weight residual 1.375 1.540 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C1C BLA A1816 " pdb=" NC BLA A1816 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" NB BLA C1313 " pdb=" C4B BLA C1313 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C4C BLA B1313 " pdb=" NC BLA B1313 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 52681 not shown) Histogram of bond angle deviations from ideal: 91.20 - 99.88: 9 99.88 - 108.55: 16865 108.55 - 117.23: 51236 117.23 - 125.90: 25803 125.90 - 134.57: 493 Bond angle restraints: 94406 Sorted by residual: angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 134.57 -20.17 2.30e+00 1.89e-01 7.69e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 134.39 -19.99 2.30e+00 1.89e-01 7.56e+01 angle pdb=" CA ASP B 80 " pdb=" C ASP B 80 " pdb=" O ASP B 80 " ideal model delta sigma weight residual 121.47 113.98 7.49 1.15e+00 7.56e-01 4.24e+01 angle pdb=" N VAL B 70 " pdb=" CA VAL B 70 " pdb=" HA VAL B 70 " ideal model delta sigma weight residual 110.00 92.08 17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" C11 EIC C1314 " pdb=" C10 EIC C1314 " pdb=" C9 EIC C1314 " ideal model delta sigma weight residual 127.32 109.40 17.92 3.00e+00 1.11e-01 3.57e+01 ... (remaining 94401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 23561 17.82 - 35.65: 1924 35.65 - 53.47: 538 53.47 - 71.30: 149 71.30 - 89.12: 24 Dihedral angle restraints: 26196 sinusoidal: 14624 harmonic: 11572 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 149.95 -56.95 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual -180.00 -148.55 -31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA VAL B 130 " pdb=" C VAL B 130 " pdb=" N CYS B 131 " pdb=" CA CYS B 131 " ideal model delta harmonic sigma weight residual 180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 26193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.554: 4390 0.554 - 1.109: 0 1.109 - 1.663: 0 1.663 - 2.218: 0 2.218 - 2.772: 1 Chirality restraints: 4391 Sorted by residual: chirality pdb=" CA VAL B 70 " pdb=" N VAL B 70 " pdb=" C VAL B 70 " pdb=" CB VAL B 70 " both_signs ideal model delta sigma weight residual False 2.44 -0.33 2.77 2.00e-01 2.50e+01 1.92e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4388 not shown) Planarity restraints: 7939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA C1313 " 0.136 2.00e-02 2.50e+03 1.46e-01 5.34e+02 pdb=" C1A BLA C1313 " -0.333 2.00e-02 2.50e+03 pdb=" C1D BLA C1313 " 0.031 2.00e-02 2.50e+03 pdb=" C2D BLA C1313 " -0.034 2.00e-02 2.50e+03 pdb=" C3D BLA C1313 " 0.026 2.00e-02 2.50e+03 pdb=" C4D BLA C1313 " 0.133 2.00e-02 2.50e+03 pdb=" CAD BLA C1313 " -0.009 2.00e-02 2.50e+03 pdb=" CHA BLA C1313 " 0.207 2.00e-02 2.50e+03 pdb=" CHD BLA C1313 " -0.012 2.00e-02 2.50e+03 pdb=" CMD BLA C1313 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1313 " 0.131 2.00e-02 2.50e+03 1.44e-01 5.17e+02 pdb=" C1A BLA B1313 " -0.331 2.00e-02 2.50e+03 pdb=" C1D BLA B1313 " 0.030 2.00e-02 2.50e+03 pdb=" C2D BLA B1313 " -0.035 2.00e-02 2.50e+03 pdb=" C3D BLA B1313 " 0.026 2.00e-02 2.50e+03 pdb=" C4D BLA B1313 " 0.131 2.00e-02 2.50e+03 pdb=" CAD BLA B1313 " -0.013 2.00e-02 2.50e+03 pdb=" CHA BLA B1313 " 0.201 2.00e-02 2.50e+03 pdb=" CHD BLA B1313 " 0.002 2.00e-02 2.50e+03 pdb=" CMD BLA B1313 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA C1313 " 0.083 2.00e-02 2.50e+03 9.19e-02 2.11e+02 pdb=" OB BLA C1313 " -0.007 2.00e-02 2.50e+03 pdb=" C1B BLA C1313 " 0.086 2.00e-02 2.50e+03 pdb=" C2B BLA C1313 " 0.014 2.00e-02 2.50e+03 pdb=" C3B BLA C1313 " -0.027 2.00e-02 2.50e+03 pdb=" C4A BLA C1313 " -0.208 2.00e-02 2.50e+03 pdb=" C4B BLA C1313 " 0.015 2.00e-02 2.50e+03 pdb=" CAB BLA C1313 " -0.089 2.00e-02 2.50e+03 pdb=" CHB BLA C1313 " 0.133 2.00e-02 2.50e+03 pdb=" CMB BLA C1313 " 0.000 2.00e-02 2.50e+03 ... (remaining 7936 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 7686 2.27 - 2.85: 114734 2.85 - 3.44: 131629 3.44 - 4.02: 190453 4.02 - 4.60: 285993 Nonbonded interactions: 730495 Sorted by model distance: nonbonded pdb="HH11 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.691 1.850 nonbonded pdb=" OE2 GLU B 725 " pdb=" HE2 HIS B1064 " model vdw 1.694 1.850 nonbonded pdb=" O ASP A 253 " pdb=" H GLY A 257 " model vdw 1.695 1.850 nonbonded pdb=" OD2 ASP C 40 " pdb="HH12 ARG C 44 " model vdw 1.710 1.850 nonbonded pdb=" OG SER A1051 " pdb=" HD1 HIS A1064 " model vdw 1.711 1.850 ... (remaining 730490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 77 \ through 79 or (resid 80 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 81 through 142 or (resid 143 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or na \ me HG13 or name HG21 or name HG22 or name HG23)) or resid 144 through 152 or (re \ sid 153 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HE1 or name HE2 or name HE3)) or resid 154 through 244 or (resid 245 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name HA or name HB2 or name HB3 or name HD1 or name H \ D2 or name HE1)) or resid 246 through 256 or (resid 257 and (name N or name CA o \ r name C or name O or name HA2 or name HA3)) or resid 258 through 1140 or resid \ 1804 through 1811 or resid 1813 through 1814)) selection = (chain 'B' and (resid 14 through 70 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 78 through 148 or ( \ resid 149 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) o \ r resid 150 through 226 or (resid 227 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name H \ G12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 228 through 6 \ 02 or (resid 603 and (name N or name CA or name C or name O or name CB or name C \ G or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name H \ D21)) or resid 604 through 618 or (resid 632 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or \ name HG21 or name HG22 or name HG23)) or resid 633 through 829 or (resid 835 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) \ or resid 836 through 1140 or resid 1301 through 1308 or resid 1310 through 1311) \ ) selection = (chain 'C' and (resid 14 through 70 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 78 through 142 or ( \ resid 143 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 144 through 148 or (resid 149 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or \ name H or name HA or name HB2 or name HB3 or name HD21)) or resid 150 through 2 \ 26 or (resid 227 and (name N or name CA or name C or name O or name CB or name C \ G1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or n \ ame HG21 or name HG22 or name HG23)) or resid 228 through 602 or (resid 603 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 604 th \ rough 618 or (resid 632 and (name N or name CA or name C or name O or name CB or \ name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG2 \ 2 or name HG23)) or resid 633 through 829 or (resid 835 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name CE or name NZ or nam \ e HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or \ name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 836 through \ 1140 or resid 1302 through 1309 or resid 1311 through 1312)) } 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' } 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=0.00 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: 2.300 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: 0.600 Extract box with map and model: 10.570 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 123.780 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.012 0.165 27521 Z= 0.796 Angle : 0.881 20.175 37442 Z= 0.401 Chirality : 0.066 2.772 4391 Planarity : 0.005 0.146 4758 Dihedral : 13.723 89.124 10890 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.24 % Allowed : 0.38 % Favored : 99.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.92 (0.14), residues: 3285 helix: 0.57 (0.20), residues: 732 sheet: -0.33 (0.18), residues: 741 loop : -1.23 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.007 0.001 HIS B 207 PHE 0.014 0.001 PHE A 79 TYR 0.021 0.001 TYR A 365 ARG 0.015 0.001 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6679 (m) REVERT: C 1002 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7566 (tp-100) REVERT: B 78 ARG cc_start: 0.6091 (ttp80) cc_final: 0.5805 (ttp80) REVERT: B 170 TYR cc_start: 0.7245 (t80) cc_final: 0.6966 (t80) REVERT: A 389 ASP cc_start: 0.7610 (m-30) cc_final: 0.7343 (m-30) REVERT: A 1101 HIS cc_start: 0.7927 (m90) cc_final: 0.7580 (m90) outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 2.0861 time to fit residues: 509.3598 Evaluate side-chains 121 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain A residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.6980 chunk 250 optimal weight: 0.3980 chunk 138 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 192 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS B 607 GLN A 99 ASN A 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27521 Z= 0.170 Angle : 0.510 14.412 37442 Z= 0.261 Chirality : 0.053 1.996 4391 Planarity : 0.003 0.068 4758 Dihedral : 8.378 89.083 5008 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.38 % Allowed : 4.48 % Favored : 95.14 % Cbeta Deviations : 0.03 % 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: -0.73 (0.14), residues: 3285 helix: 0.85 (0.20), residues: 738 sheet: -0.21 (0.18), residues: 722 loop : -1.18 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.004 0.000 HIS C 69 PHE 0.013 0.001 PHE A 643 TYR 0.017 0.001 TYR B 365 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: C 869 MET cc_start: 0.8455 (mtp) cc_final: 0.8237 (mtp) REVERT: C 1002 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7515 (tp-100) REVERT: B 170 TYR cc_start: 0.7344 (t80) cc_final: 0.6988 (t80) REVERT: B 212 LEU cc_start: 0.8143 (tp) cc_final: 0.7886 (tt) REVERT: A 389 ASP cc_start: 0.7584 (m-30) cc_final: 0.7321 (m-30) REVERT: A 1101 HIS cc_start: 0.7948 (m90) cc_final: 0.7604 (m90) outliers start: 11 outliers final: 2 residues processed: 134 average time/residue: 2.0095 time to fit residues: 329.9033 Evaluate side-chains 120 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain A residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 240 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27521 Z= 0.190 Angle : 0.490 14.126 37442 Z= 0.251 Chirality : 0.051 1.841 4391 Planarity : 0.003 0.054 4758 Dihedral : 7.309 82.789 5005 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.52 % Allowed : 5.28 % Favored : 94.20 % Cbeta Deviations : 0.03 % 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: -0.62 (0.14), residues: 3285 helix: 0.91 (0.20), residues: 740 sheet: -0.08 (0.18), residues: 723 loop : -1.13 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.008 0.001 HIS C 146 PHE 0.014 0.001 PHE A 643 TYR 0.016 0.001 TYR B 365 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 3.089 Fit side-chains revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: C 1002 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7492 (tp-100) REVERT: B 170 TYR cc_start: 0.7400 (t80) cc_final: 0.7072 (t80) REVERT: B 212 LEU cc_start: 0.8060 (tp) cc_final: 0.7770 (tt) REVERT: A 389 ASP cc_start: 0.7644 (m-30) cc_final: 0.7387 (m-30) REVERT: A 405 ASP cc_start: 0.7728 (m-30) cc_final: 0.7319 (m-30) REVERT: A 1101 HIS cc_start: 0.7954 (m90) cc_final: 0.7603 (m90) REVERT: A 1139 ASP cc_start: 0.8295 (t0) cc_final: 0.7928 (m-30) outliers start: 15 outliers final: 5 residues processed: 137 average time/residue: 1.8515 time to fit residues: 315.6490 Evaluate side-chains 124 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 969 ASN B 969 ASN A 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 27521 Z= 0.322 Angle : 0.533 14.921 37442 Z= 0.274 Chirality : 0.052 1.837 4391 Planarity : 0.004 0.046 4758 Dihedral : 6.801 68.652 5005 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.80 % Allowed : 6.70 % Favored : 92.50 % Cbeta Deviations : 0.03 % 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: -0.67 (0.14), residues: 3285 helix: 0.73 (0.20), residues: 743 sheet: -0.01 (0.18), residues: 731 loop : -1.15 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 64 HIS 0.003 0.001 HIS A1064 PHE 0.014 0.001 PHE B 86 TYR 0.024 0.001 TYR B 365 ARG 0.003 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: C 1002 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7543 (tp-100) REVERT: A 389 ASP cc_start: 0.7873 (m-30) cc_final: 0.7577 (m-30) outliers start: 23 outliers final: 12 residues processed: 146 average time/residue: 1.9513 time to fit residues: 349.0421 Evaluate side-chains 127 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 27521 Z= 0.400 Angle : 0.558 14.975 37442 Z= 0.288 Chirality : 0.053 1.783 4391 Planarity : 0.004 0.042 4758 Dihedral : 6.618 65.081 5005 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.94 % Allowed : 7.81 % Favored : 91.25 % Cbeta Deviations : 0.03 % 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: -0.81 (0.14), residues: 3285 helix: 0.51 (0.20), residues: 744 sheet: -0.02 (0.18), residues: 743 loop : -1.22 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 64 HIS 0.004 0.001 HIS C1064 PHE 0.017 0.001 PHE B 86 TYR 0.027 0.001 TYR B 365 ARG 0.004 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: B 947 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8120 (mtpt) REVERT: A 389 ASP cc_start: 0.7933 (m-30) cc_final: 0.7648 (m-30) outliers start: 27 outliers final: 15 residues processed: 142 average time/residue: 1.7355 time to fit residues: 306.6917 Evaluate side-chains 128 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.7980 chunk 287 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27521 Z= 0.191 Angle : 0.503 14.034 37442 Z= 0.258 Chirality : 0.051 1.796 4391 Planarity : 0.003 0.040 4758 Dihedral : 6.253 64.606 5005 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.69 % Allowed : 8.51 % Favored : 90.80 % Cbeta Deviations : 0.03 % 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: -0.70 (0.14), residues: 3285 helix: 0.62 (0.20), residues: 754 sheet: 0.01 (0.18), residues: 735 loop : -1.14 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.003 0.000 HIS B1064 PHE 0.012 0.001 PHE A 643 TYR 0.016 0.001 TYR B 365 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: C 1002 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7497 (tp-100) REVERT: A 389 ASP cc_start: 0.7855 (m-30) cc_final: 0.7565 (m-30) REVERT: A 1101 HIS cc_start: 0.7976 (m90) cc_final: 0.7591 (m90) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 1.7584 time to fit residues: 304.4137 Evaluate side-chains 124 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27521 Z= 0.274 Angle : 0.512 14.260 37442 Z= 0.263 Chirality : 0.051 1.780 4391 Planarity : 0.003 0.039 4758 Dihedral : 6.100 62.756 5005 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.08 % Allowed : 8.47 % Favored : 90.45 % Cbeta Deviations : 0.03 % 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: -0.70 (0.14), residues: 3285 helix: 0.61 (0.20), residues: 760 sheet: 0.01 (0.18), residues: 732 loop : -1.15 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 PHE 0.012 0.001 PHE B 86 TYR 0.021 0.001 TYR B 365 ARG 0.003 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 CYS cc_start: 0.3639 (m) cc_final: 0.3333 (m) REVERT: C 675 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: A 389 ASP cc_start: 0.7828 (m-30) cc_final: 0.7559 (m-30) REVERT: A 1101 HIS cc_start: 0.7986 (m90) cc_final: 0.7595 (m90) outliers start: 31 outliers final: 15 residues processed: 144 average time/residue: 1.7254 time to fit residues: 314.3300 Evaluate side-chains 126 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 157 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 250 optimal weight: 0.0870 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27521 Z= 0.237 Angle : 0.512 14.501 37442 Z= 0.264 Chirality : 0.051 1.788 4391 Planarity : 0.003 0.038 4758 Dihedral : 6.017 61.648 5005 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.76 % Allowed : 9.17 % Favored : 90.07 % Cbeta Deviations : 0.03 % 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: -0.68 (0.14), residues: 3285 helix: 0.64 (0.20), residues: 761 sheet: 0.01 (0.18), residues: 726 loop : -1.14 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.002 0.000 HIS B1064 PHE 0.013 0.001 PHE A 643 TYR 0.019 0.001 TYR B 365 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: C 1002 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7513 (tp-100) REVERT: A 389 ASP cc_start: 0.7816 (m-30) cc_final: 0.7555 (m-30) REVERT: A 1101 HIS cc_start: 0.7992 (m90) cc_final: 0.7602 (m90) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 1.8093 time to fit residues: 296.5874 Evaluate side-chains 124 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 296 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 267 optimal weight: 0.0470 chunk 280 optimal weight: 0.9990 chunk 295 optimal weight: 0.5980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C1002 GLN B 164 ASN B 641 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27521 Z= 0.165 Angle : 0.486 14.031 37442 Z= 0.249 Chirality : 0.051 1.796 4391 Planarity : 0.003 0.038 4758 Dihedral : 5.796 60.876 5005 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.56 % Allowed : 9.27 % Favored : 90.17 % Cbeta Deviations : 0.03 % 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: -0.58 (0.14), residues: 3285 helix: 0.78 (0.20), residues: 761 sheet: 0.05 (0.18), residues: 710 loop : -1.07 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.000 HIS B 207 PHE 0.014 0.001 PHE A 643 TYR 0.014 0.001 TYR B 365 ARG 0.002 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1002 GLN cc_start: 0.7781 (tp40) cc_final: 0.7525 (tp-100) REVERT: A 389 ASP cc_start: 0.7793 (m-30) cc_final: 0.7530 (m-30) REVERT: A 1101 HIS cc_start: 0.7977 (m90) cc_final: 0.7593 (m90) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 1.7880 time to fit residues: 290.5411 Evaluate side-chains 123 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 328 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27521 Z= 0.199 Angle : 0.491 14.023 37442 Z= 0.252 Chirality : 0.051 1.793 4391 Planarity : 0.003 0.037 4758 Dihedral : 5.724 59.942 5005 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.49 % Allowed : 9.48 % Favored : 90.03 % Cbeta Deviations : 0.03 % 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: -0.58 (0.14), residues: 3285 helix: 0.76 (0.20), residues: 767 sheet: 0.06 (0.18), residues: 714 loop : -1.09 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.002 0.000 HIS B 207 PHE 0.015 0.001 PHE A 643 TYR 0.017 0.001 TYR B 365 ARG 0.002 0.000 ARG C 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 427 CYS cc_start: 0.3221 (m) cc_final: 0.2965 (m) REVERT: C 1002 GLN cc_start: 0.7787 (tp40) cc_final: 0.7516 (tp-100) REVERT: A 389 ASP cc_start: 0.7793 (m-30) cc_final: 0.7528 (m-30) REVERT: A 1101 HIS cc_start: 0.7976 (m90) cc_final: 0.7589 (m90) REVERT: A 1125 ASN cc_start: 0.8255 (p0) cc_final: 0.8052 (p0) outliers start: 14 outliers final: 13 residues processed: 126 average time/residue: 1.7490 time to fit residues: 274.2657 Evaluate side-chains 124 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 987 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.084326 restraints weight = 116416.207| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.46 r_work: 0.2929 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27521 Z= 0.162 Angle : 0.476 13.734 37442 Z= 0.244 Chirality : 0.051 1.796 4391 Planarity : 0.003 0.037 4758 Dihedral : 5.528 58.799 5005 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.62 % Allowed : 9.41 % Favored : 89.97 % Cbeta Deviations : 0.03 % 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: -0.51 (0.14), residues: 3285 helix: 0.84 (0.20), residues: 770 sheet: 0.13 (0.19), residues: 706 loop : -1.06 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.000 HIS B 207 PHE 0.014 0.001 PHE A 643 TYR 0.013 0.001 TYR B 365 ARG 0.002 0.000 ARG C 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8687.38 seconds wall clock time: 151 minutes 56.71 seconds (9116.71 seconds total)