Starting phenix.real_space_refine (version: dev) on Fri Feb 24 21:28:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/02_2023/7lww_23559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/02_2023/7lww_23559.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/7lww_23559/02_2023/7lww_23559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/02_2023/7lww_23559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/02_2023/7lww_23559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/02_2023/7lww_23559.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= 0.076 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 Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23786 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7708 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7702 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7676 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 53 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.46, per 1000 atoms: 0.57 Number of scatterers: 23786 At special positions: 0 Unit cell: (129.349, 135.763, 192.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 4613 8.00 N 3896 7.00 C 15176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.01 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 282 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 616 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 3.4 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 46 sheets defined 27.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.832A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.749A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.814A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.610A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.789A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.802A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.562A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.626A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.173A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.916A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.925A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.546A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.285A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.947A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.847A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.814A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.175A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.560A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.719A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.377A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.249A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.237A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.926A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.794A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.515A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.386A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.636A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.452A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.549A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.285A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.153A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.926A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.957A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.040A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.850A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.492A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.492A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.590A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.774A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.466A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.756A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.545A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.576A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.386A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.366A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.553A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 9.120A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.827A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.678A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.714A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.438A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.378A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.378A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.866A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.236A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.870A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.77 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6353 1.33 - 1.46: 4477 1.46 - 1.58: 13344 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24299 Sorted by residual: bond pdb=" C4 NAG L 1 " pdb=" O4 NAG L 1 " ideal model delta sigma weight residual 1.423 1.482 -0.059 1.00e-02 1.00e+04 3.50e+01 bond pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sigma weight residual 1.423 1.476 -0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 1.423 1.474 -0.051 1.00e-02 1.00e+04 2.55e+01 bond pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 1.423 1.473 -0.050 1.00e-02 1.00e+04 2.52e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.10e-02 8.26e+03 2.52e+01 ... (remaining 24294 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.91: 266 103.91 - 111.74: 9444 111.74 - 119.58: 10496 119.58 - 127.42: 12703 127.42 - 135.25: 161 Bond angle restraints: 33070 Sorted by residual: angle pdb=" C2 NAG C1306 " pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 109.64 122.26 -12.62 5.38e-01 3.45e+00 5.51e+02 angle pdb=" C2 NAG B1303 " pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 109.64 121.86 -12.22 5.38e-01 3.45e+00 5.16e+02 angle pdb=" C2 NAG A1302 " pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 109.64 119.76 -10.12 5.38e-01 3.45e+00 3.54e+02 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.41 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 ... (remaining 33065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 13430 18.05 - 36.09: 703 36.09 - 54.14: 123 54.14 - 72.18: 43 72.18 - 90.23: 23 Dihedral angle restraints: 14322 sinusoidal: 5655 harmonic: 8667 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.26 -88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.06 63.06 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" C ASP C 198 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " ideal model delta harmonic sigma weight residual -122.60 -138.15 15.55 0 2.50e+00 1.60e-01 3.87e+01 ... (remaining 14319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 3916 0.279 - 0.558: 25 0.558 - 0.838: 1 0.838 - 1.117: 0 1.117 - 1.396: 3 Chirality restraints: 3945 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.01e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.78e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.57e+01 ... (remaining 3942 not shown) Planarity restraints: 4233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.375 2.00e-02 2.50e+03 2.01e-01 1.01e+03 pdb=" CG TRP C 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.181 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.144 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.291 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.227 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.085 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.207 2.00e-02 2.50e+03 1.27e-01 3.23e+02 pdb=" CG TYR C 904 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.103 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.093 2.00e-02 2.50e+03 1.05e-01 1.38e+02 pdb=" CG ASN A 331 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.172 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.125 2.00e-02 2.50e+03 ... (remaining 4230 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11406 2.99 - 3.47: 22314 3.47 - 3.94: 39320 3.94 - 4.42: 43733 4.42 - 4.90: 73753 Nonbonded interactions: 190526 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.511 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.523 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.525 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.530 2.440 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.532 2.440 ... (remaining 190521 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 479 or (resid 480 and (name N or name CA or name C or name O o \ r name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or na \ me C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 855 through 866 or (resid 867 through 868 and (name N or name CA \ or name C or name O or name CB )) or resid 869 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 through 1144 o \ r (resid 1145 through 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 567 or (resid 568 and (name N or name CA or name C or n \ ame O or name CB )) or resid 569 through 582 or (resid 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 618 or \ (resid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 \ through 676 or resid 690 through 744 or (resid 745 and (name N or name CA or na \ me C or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N \ or name CA or name C or name O or name CB )) or resid 749 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 or (re \ sid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 th \ rough 827 or resid 855 through 866 or (resid 867 through 868 and (name N or name \ CA or name C or name O or name CB )) or resid 869 through 1091 or (resid 1092 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1093 through 11 \ 43 or (resid 1144 through 1146 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 238 or (resid 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or name \ C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N or \ name CA or name C or name O or name CB )) or resid 529 through 567 or (resid 56 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 569 through \ 582 or (resid 583 and (name N or name CA or name C or name O or name CB )) or re \ sid 584 through 585 or (resid 586 and (name N or name CA or name C or name O or \ name CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 1091 or (resid 1 \ 092 and (name N or name CA or name C or name O or name CB )) or resid 1093 throu \ gh 1141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) \ or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C or na \ me O or name CB )) or resid 1147 or resid 1301 through 1308)) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 15176 2.51 5 N 3896 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.090 Check model and map are aligned: 0.360 Process input model: 63.660 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.013 0.059 24299 Z= 0.850 Angle : 1.776 12.625 33070 Z= 1.218 Chirality : 0.102 1.396 3945 Planarity : 0.014 0.206 4195 Dihedral : 12.619 90.229 8631 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.29 % Favored : 94.40 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.18 % 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: -0.82 (0.14), residues: 2928 helix: -1.07 (0.16), residues: 697 sheet: 0.52 (0.21), residues: 559 loop : -0.62 (0.14), residues: 1672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 357 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 368 average time/residue: 1.1479 time to fit residues: 498.6027 Evaluate side-chains 181 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.3204 time to fit residues: 4.7594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 0.2980 chunk 141 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 314 GLN A 317 ASN A 913 GLN A 957 GLN A 969 ASN A1010 GLN A1101 HIS B 540 ASN B 675 GLN B 755 GLN B1088 HIS C 81 ASN C 613 GLN C 764 ASN C 779 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24299 Z= 0.210 Angle : 0.630 9.967 33070 Z= 0.344 Chirality : 0.047 0.385 3945 Planarity : 0.004 0.066 4195 Dihedral : 5.889 24.947 3482 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.86 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2928 helix: 1.14 (0.20), residues: 680 sheet: 0.59 (0.19), residues: 684 loop : -0.54 (0.15), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 213 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 16 residues processed: 245 average time/residue: 0.9786 time to fit residues: 291.9040 Evaluate side-chains 158 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 3.021 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.2487 time to fit residues: 6.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 0.0670 chunk 240 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN A1002 GLN A1048 HIS B 675 GLN B 755 GLN B 901 GLN B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 24299 Z= 0.300 Angle : 0.600 13.086 33070 Z= 0.320 Chirality : 0.046 0.276 3945 Planarity : 0.004 0.059 4195 Dihedral : 5.436 25.666 3482 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2928 helix: 1.47 (0.20), residues: 674 sheet: 0.48 (0.19), residues: 696 loop : -0.59 (0.15), residues: 1558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 218 average time/residue: 1.0113 time to fit residues: 269.4678 Evaluate side-chains 171 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 5 average time/residue: 0.5091 time to fit residues: 7.1990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 271 optimal weight: 0.0770 chunk 287 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 256 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 675 GLN B 755 GLN B1088 HIS C 81 ASN C 239 GLN C 690 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24299 Z= 0.198 Angle : 0.532 12.120 33070 Z= 0.283 Chirality : 0.044 0.239 3945 Planarity : 0.004 0.053 4195 Dihedral : 5.123 23.418 3482 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.13 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2928 helix: 1.76 (0.21), residues: 668 sheet: 0.40 (0.19), residues: 686 loop : -0.45 (0.15), residues: 1574 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 35 residues processed: 213 average time/residue: 0.9036 time to fit residues: 240.9275 Evaluate side-chains 181 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 5 average time/residue: 0.2895 time to fit residues: 6.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 901 GLN A 969 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN B1048 HIS B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 690 GLN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.078 24299 Z= 0.583 Angle : 0.673 10.709 33070 Z= 0.354 Chirality : 0.050 0.262 3945 Planarity : 0.004 0.055 4195 Dihedral : 5.445 26.881 3482 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2928 helix: 1.25 (0.20), residues: 672 sheet: 0.15 (0.18), residues: 720 loop : -0.69 (0.15), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 161 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 44 residues processed: 218 average time/residue: 1.0005 time to fit residues: 268.2193 Evaluate side-chains 197 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 2.921 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 37 residues processed: 8 average time/residue: 0.2905 time to fit residues: 8.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 969 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 926 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 24299 Z= 0.174 Angle : 0.533 11.560 33070 Z= 0.282 Chirality : 0.044 0.232 3945 Planarity : 0.004 0.051 4195 Dihedral : 5.036 23.462 3482 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2928 helix: 1.77 (0.21), residues: 661 sheet: 0.33 (0.19), residues: 709 loop : -0.52 (0.15), residues: 1558 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 163 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 38 residues processed: 211 average time/residue: 0.9787 time to fit residues: 255.6872 Evaluate side-chains 187 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 3 average time/residue: 0.5821 time to fit residues: 6.2005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 165 ASN A 969 ASN A1101 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN B 779 GLN B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 926 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 24299 Z= 0.328 Angle : 0.574 9.340 33070 Z= 0.301 Chirality : 0.046 0.231 3945 Planarity : 0.004 0.050 4195 Dihedral : 5.122 24.972 3482 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2928 helix: 1.66 (0.21), residues: 667 sheet: 0.33 (0.19), residues: 691 loop : -0.57 (0.15), residues: 1570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 158 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 45 residues processed: 207 average time/residue: 0.8503 time to fit residues: 222.4158 Evaluate side-chains 194 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 6 average time/residue: 0.2944 time to fit residues: 6.4911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 170 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 0.2980 chunk 195 optimal weight: 0.2980 chunk 141 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B 271 GLN B 675 GLN B 755 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 24299 Z= 0.147 Angle : 0.510 12.506 33070 Z= 0.267 Chirality : 0.043 0.203 3945 Planarity : 0.003 0.049 4195 Dihedral : 4.812 22.071 3482 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 2928 helix: 1.97 (0.21), residues: 667 sheet: 0.45 (0.19), residues: 685 loop : -0.46 (0.15), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 220 average time/residue: 0.9860 time to fit residues: 269.2656 Evaluate side-chains 181 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 2.967 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 1 average time/residue: 0.5868 time to fit residues: 6.6896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 266 optimal weight: 0.0770 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 265 optimal weight: 0.4980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 271 GLN B 675 GLN B 755 GLN B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 24299 Z= 0.155 Angle : 0.512 9.885 33070 Z= 0.268 Chirality : 0.043 0.191 3945 Planarity : 0.004 0.048 4195 Dihedral : 4.738 22.904 3482 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2928 helix: 2.00 (0.21), residues: 674 sheet: 0.49 (0.19), residues: 694 loop : -0.42 (0.16), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 159 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 40 residues processed: 206 average time/residue: 0.9300 time to fit residues: 240.0731 Evaluate side-chains 187 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 3 average time/residue: 0.3144 time to fit residues: 5.3391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 235 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 271 GLN B 675 GLN B 755 GLN C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 24299 Z= 0.250 Angle : 0.542 9.109 33070 Z= 0.284 Chirality : 0.044 0.201 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.856 23.838 3482 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2928 helix: 1.92 (0.21), residues: 677 sheet: 0.51 (0.19), residues: 690 loop : -0.47 (0.16), residues: 1561 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 38 residues processed: 189 average time/residue: 0.9426 time to fit residues: 223.8882 Evaluate side-chains 180 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 3 average time/residue: 0.2985 time to fit residues: 5.7833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 675 GLN B 755 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.175334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136979 restraints weight = 30462.356| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.85 r_work: 0.3224 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 24299 Z= 0.198 Angle : 0.518 9.031 33070 Z= 0.271 Chirality : 0.043 0.198 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.785 23.791 3482 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2928 helix: 2.00 (0.21), residues: 677 sheet: 0.51 (0.19), residues: 686 loop : -0.44 (0.16), residues: 1565 =============================================================================== Job complete usr+sys time: 5860.17 seconds wall clock time: 107 minutes 4.21 seconds (6424.21 seconds total)