Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:19:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/04_2023/7xu1_33455_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/04_2023/7xu1_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_33455/04_2023/7xu1_33455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/04_2023/7xu1_33455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/04_2023/7xu1_33455_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu1_33455/04_2023/7xu1_33455_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 chiralities: 13 Time building chain proxies: 16.47, per 1000 atoms: 0.32 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: 31.27 Conformation dependent library (CDL) restraints added in 3.6 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: 3.82 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: 19.81 Time building geometry restraints manager: 33.04 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: 19245 17.82 - 35.65: 1577 35.65 - 53.47: 226 53.47 - 71.30: 60 71.30 - 89.12: 24 Dihedral angle restraints: 21132 sinusoidal: 9560 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 21129 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: 1.890 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: 0.580 Extract box with map and model: 11.960 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 120.660 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.360 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:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.490 ------------------------------------------------------------------------------- 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 : 13.628 89.124 9519 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 % 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 *********************** 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 : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 2.1153 time to fit residues: 518.3641 Evaluate side-chains 118 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 3.033 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.9406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.8980 chunk 250 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 192 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 607 GLN A 99 ASN A 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0715 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= 0.182 Angle : 0.514 14.430 37442 Z= 0.262 Chirality : 0.053 1.980 4391 Planarity : 0.003 0.068 4758 Dihedral : 6.859 89.801 3633 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.45 % 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: -0.73 (0.14), residues: 3285 helix: 0.86 (0.20), residues: 738 sheet: -0.20 (0.18), residues: 722 loop : -1.18 (0.14), residues: 1825 *********************** 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 139 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 3.095 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 134 average time/residue: 2.0592 time to fit residues: 341.6188 Evaluate side-chains 117 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 3.071 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.4813 time to fit residues: 5.6763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 249 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 267 optimal weight: 0.0010 chunk 297 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.076 27521 Z= 0.158 Angle : 0.487 13.971 37442 Z= 0.249 Chirality : 0.052 1.871 4391 Planarity : 0.003 0.056 4758 Dihedral : 6.478 84.479 3633 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.42 % 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: -0.63 (0.14), residues: 3285 helix: 0.88 (0.20), residues: 750 sheet: -0.08 (0.18), residues: 723 loop : -1.13 (0.14), residues: 1812 *********************** 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 133 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 3.077 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 132 average time/residue: 1.8112 time to fit residues: 297.9571 Evaluate side-chains 121 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 3.095 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.4498 time to fit residues: 4.7708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 969 ASN C1002 GLN B 969 ASN A 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 27521 Z= 0.374 Angle : 0.557 15.142 37442 Z= 0.285 Chirality : 0.052 1.823 4391 Planarity : 0.004 0.048 4758 Dihedral : 6.355 68.060 3633 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.73 % 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: 0.66 (0.20), residues: 744 sheet: -0.01 (0.18), residues: 721 loop : -1.19 (0.14), residues: 1820 *********************** 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 142 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 138 average time/residue: 1.9829 time to fit residues: 336.5491 Evaluate side-chains 120 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 3.122 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.4607 time to fit residues: 6.5373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 27521 Z= 0.267 Angle : 0.516 14.562 37442 Z= 0.265 Chirality : 0.052 1.812 4391 Planarity : 0.003 0.045 4758 Dihedral : 6.115 67.125 3633 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.73 % 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: 0.64 (0.20), residues: 751 sheet: 0.01 (0.18), residues: 725 loop : -1.15 (0.14), residues: 1809 *********************** 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 138 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 136 average time/residue: 1.7992 time to fit residues: 303.9124 Evaluate side-chains 119 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 3.115 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.4428 time to fit residues: 5.6556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 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: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 27521 Z= 0.294 Angle : 0.525 14.505 37442 Z= 0.269 Chirality : 0.052 1.791 4391 Planarity : 0.003 0.042 4758 Dihedral : 5.955 64.939 3633 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.69 % 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: 752 sheet: 0.00 (0.18), residues: 733 loop : -1.15 (0.14), residues: 1800 *********************** 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 133 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 130 average time/residue: 1.8811 time to fit residues: 306.1211 Evaluate side-chains 120 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 3.067 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.4749 time to fit residues: 5.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 180 optimal weight: 0.4980 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 27521 Z= 0.199 Angle : 0.498 13.965 37442 Z= 0.254 Chirality : 0.051 1.803 4391 Planarity : 0.003 0.040 4758 Dihedral : 5.748 64.078 3633 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.73 % 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: -0.64 (0.14), residues: 3285 helix: 0.73 (0.20), residues: 755 sheet: 0.02 (0.18), residues: 710 loop : -1.12 (0.14), residues: 1820 *********************** 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 131 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 1.9176 time to fit residues: 313.7576 Evaluate side-chains 122 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 3.065 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.4864 time to fit residues: 5.7327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 27521 Z= 0.354 Angle : 0.545 14.583 37442 Z= 0.279 Chirality : 0.052 1.775 4391 Planarity : 0.003 0.040 4758 Dihedral : 5.878 61.854 3633 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.73 % 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: -0.69 (0.14), residues: 3285 helix: 0.64 (0.20), residues: 749 sheet: -0.01 (0.18), residues: 726 loop : -1.13 (0.14), residues: 1810 *********************** 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 136 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 1.8152 time to fit residues: 299.2330 Evaluate side-chains 120 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 3.059 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.4405 time to fit residues: 5.5903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 280 optimal weight: 0.6980 chunk 295 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN C1002 GLN B 164 ASN A1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 27521 Z= 0.194 Angle : 0.506 14.060 37442 Z= 0.258 Chirality : 0.051 1.795 4391 Planarity : 0.003 0.039 4758 Dihedral : 5.767 61.335 3633 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.69 % 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: -0.64 (0.14), residues: 3285 helix: 0.71 (0.20), residues: 759 sheet: 0.03 (0.18), residues: 718 loop : -1.12 (0.14), residues: 1808 *********************** 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 128 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 1.9149 time to fit residues: 303.4461 Evaluate side-chains 120 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 3.071 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.4940 time to fit residues: 4.8036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 148 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 261 optimal weight: 0.0010 chunk 27 optimal weight: 0.0970 chunk 202 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN B 641 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1464 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= 0.171 Angle : 0.497 13.859 37442 Z= 0.254 Chirality : 0.051 1.787 4391 Planarity : 0.003 0.039 4758 Dihedral : 5.662 60.613 3633 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.56 % 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: -0.57 (0.14), residues: 3285 helix: 0.82 (0.20), residues: 758 sheet: 0.06 (0.19), residues: 710 loop : -1.09 (0.14), residues: 1817 ********************** 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 126 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 125 average time/residue: 1.8887 time to fit residues: 294.2982 Evaluate side-chains 119 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.4594 time to fit residues: 4.7555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 241 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.083295 restraints weight = 116333.130| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.48 r_work: 0.2914 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 27521 Z= 0.201 Angle : 0.497 13.881 37442 Z= 0.254 Chirality : 0.051 1.794 4391 Planarity : 0.003 0.039 4758 Dihedral : 5.618 59.682 3633 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.52 % 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: -0.57 (0.14), residues: 3285 helix: 0.81 (0.20), residues: 762 sheet: 0.11 (0.19), residues: 700 loop : -1.11 (0.14), residues: 1823 =============================================================================== Job complete usr+sys time: 8829.41 seconds wall clock time: 156 minutes 24.91 seconds (9384.91 seconds total)