Starting phenix.real_space_refine (version: dev) on Sat Feb 25 00:04:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/02_2023/7cn9_30419.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/02_2023/7cn9_30419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/02_2023/7cn9_30419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/02_2023/7cn9_30419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/02_2023/7cn9_30419.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/02_2023/7cn9_30419.pdb" } resolution = 4.7 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= 0.001 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 GLU 169": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24052 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7727 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 48, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 7674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7674 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 48, 'TRANS': 961} Chain breaks: 10 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 164 Chain: "C" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7889 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 49, 'TRANS': 987} Chain breaks: 6 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 152 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: "X" 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "Z" 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: "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: "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: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: "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: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.13, per 1000 atoms: 0.55 Number of scatterers: 24052 At special positions: 0 Unit cell: (152.52, 159.08, 167.28, 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 106 16.00 O 4700 8.00 N 3942 7.00 C 15304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 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=2.02 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=2.02 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 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.89 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=1.93 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 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=2.26 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23770 O5 NAG A1203 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA h 3 " - " MAN h 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG k 1 " - " NAG k 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " BETA1-6 " NAG k 1 " - " FUC k 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1201 " - " ASN A 616 " " NAG A1202 " - " ASN A 657 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A1098 " " NAG A1205 " - " ASN A1134 " " NAG A1206 " - " ASN A 122 " " NAG A1207 " - " ASN A 282 " " NAG B1201 " - " ASN B 331 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 616 " " NAG B1204 " - " ASN B 657 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B1098 " " NAG B1207 " - " ASN B 234 " " NAG B1208 " - " ASN B 165 " " NAG B1209 " - " ASN B 74 " " NAG C1201 " - " ASN C1134 " " NAG C1202 " - " ASN C 709 " " NAG C1203 " - " ASN C 657 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 61 " " NAG C1207 " - " ASN C 331 " " NAG E 1 " - " ASN C1074 " " NAG H 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 801 " " NAG V 1 " - " ASN A 331 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN C 717 " " NAG Z 1 " - " ASN B1134 " " NAG d 1 " - " ASN B1074 " " NAG f 1 " - " ASN B 801 " " NAG h 1 " - " ASN B 282 " " NAG k 1 " - " ASN C 165 " " NAG p 1 " - " ASN C 801 " Time building additional restraints: 10.97 Conformation dependent library (CDL) restraints added in 3.5 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 47 sheets defined 23.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.541A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.021A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.736A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.714A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 940 removed outlier: 6.068A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.512A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.586A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.785A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.456A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.195A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.081A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.485A 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.540A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.767A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.290A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.866A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 940 removed outlier: 6.380A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.883A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 6.078A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.062A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.513A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 removed outlier: 3.901A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.012A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 572 through 573 removed outlier: 7.000A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.546A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 724 through 728 removed outlier: 3.629A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A1049 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.604A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 5.419A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.745A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 192 through 194 removed outlier: 3.876A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.842A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.644A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.879A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC7, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC8, first strand: chain 'B' and resid 612 through 613 removed outlier: 3.703A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 659 through 660 removed outlier: 3.528A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.162A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1088 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.236A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 4.299A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.710A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 326 through 328 removed outlier: 7.313A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.831A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 644 through 645 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.700A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 727 removed outlier: 3.712A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 5.272A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1096 698 hydrogen bonds defined for protein. 1932 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: 9.15 Time building geometry restraints manager: 11.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7598 1.34 - 1.47: 6253 1.47 - 1.59: 10581 1.59 - 1.72: 3 1.72 - 1.85: 135 Bond restraints: 24570 Sorted by residual: bond pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 1.469 1.700 -0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 1.469 1.700 -0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 bond pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.09e+01 ... (remaining 24565 not shown) Histogram of bond angle deviations from ideal: 96.89 - 105.63: 528 105.63 - 114.37: 14807 114.37 - 123.11: 16370 123.11 - 131.85: 1751 131.85 - 140.60: 27 Bond angle restraints: 33483 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 119.84 140.60 -20.76 1.25e+00 6.40e-01 2.76e+02 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 139.73 -19.89 1.25e+00 6.40e-01 2.53e+02 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 98.17 13.83 1.40e+00 5.10e-01 9.76e+01 angle pdb=" CA PRO C 330 " pdb=" N PRO C 330 " pdb=" CD PRO C 330 " ideal model delta sigma weight residual 112.00 99.76 12.24 1.40e+00 5.10e-01 7.64e+01 angle pdb=" C SER B 172 " pdb=" N GLN B 173 " pdb=" CA GLN B 173 " ideal model delta sigma weight residual 122.89 115.80 7.09 1.12e+00 7.97e-01 4.00e+01 ... (remaining 33478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12746 17.93 - 35.86: 1438 35.86 - 53.78: 240 53.78 - 71.71: 39 71.71 - 89.64: 31 Dihedral angle restraints: 14494 sinusoidal: 5610 harmonic: 8884 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.55 -80.45 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -6.43 -79.57 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 14491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4007 0.199 - 0.397: 23 0.397 - 0.596: 0 0.596 - 0.794: 3 0.794 - 0.993: 2 Chirality restraints: 4035 Sorted by residual: chirality pdb=" C1 BMA p 3 " pdb=" O4 NAG p 2 " pdb=" C2 BMA p 3 " pdb=" O5 BMA p 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.75e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.38e+01 ... (remaining 4032 not shown) Planarity restraints: 4286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " -0.332 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG V 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.275 2.00e-02 2.50e+03 2.30e-01 6.59e+02 pdb=" C7 NAG X 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.386 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.257 2.00e-02 2.50e+03 2.15e-01 5.76e+02 pdb=" C7 NAG p 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.358 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 4283 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 570 2.52 - 3.12: 22695 3.12 - 3.71: 37724 3.71 - 4.31: 50734 4.31 - 4.90: 76530 Nonbonded interactions: 188253 Sorted by model distance: nonbonded pdb=" O LEU C 455 " pdb=" CD1 PHE C 456 " model vdw 1.927 3.340 nonbonded pdb=" CZ PHE B 86 " pdb=" N GLY B 89 " model vdw 1.988 3.420 nonbonded pdb=" O SER C1003 " pdb=" OG1 THR C1006 " model vdw 2.004 2.440 nonbonded pdb=" O SER B1003 " pdb=" OG1 THR B1006 " model vdw 2.021 2.440 nonbonded pdb=" NE2 GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 2.026 2.520 ... (remaining 188248 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 95 or (resid 96 throu \ gh 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (r \ esid 99 through 100 and (name N or name CA or name C or name O or name CB )) or \ resid 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 through 104 or (resid 105 and (name N or name CA or name C or name \ O or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 140 or (resid 141 and (nam \ e N or name CA or name C or name O or name CB )) or resid 142 through 155 or (re \ sid 156 and (name N or name CA or name C or name O or name CB )) or resid 157 th \ rough 159 or resid 165 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 194 or (resid 195 through 198 and (name N \ or name CA or name C or name O or name CB )) or resid 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 236 or (re \ sid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 or \ (resid 239 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 0 through 243 or resid 264 through 331 or (resid 332 through 333 and (name N or \ name CA or name C or name O or name CB )) or resid 334 or (resid 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 343 or resid \ 355 through 363 or (resid 364 and (name N or name CA or name C or name O or name \ CB )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 373 or (resid 374 and (name N or nam \ e CA or name C or name O or name CB )) or resid 375 through 407 or (resid 408 an \ d (name N or name CA or name C or name O or name CB )) or resid 409 through 442 \ or resid 455 or (resid 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 496 or (resid 497 through 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 through 500 or resid 503 through 50 \ 4 or (resid 505 and (name N or name CA or name C or name O or name CB )) or resi \ d 506 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 620 or resid 640 through 672 or resid 687 through \ 1140 or resid 1201 through 1207)) selection = (chain 'B' and (resid 27 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 159 or resid 165 t \ hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 189 or (resid 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 or (resid 212 through 215 and (name N or n \ ame CA or name C or name O or name CB )) or resid 216 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or \ resid 291 through 363 or (resid 364 and (name N or name CA or name C or name O o \ r name CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or na \ me C or name O or name CB )) or resid 375 through 442 or resid 452 or resid 454 \ or resid 462 through 463 or resid 492 through 496 or (resid 497 through 498 and \ (name N or name CA or name C or name O or name CB )) or resid 499 through 508 or \ (resid 509 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 0 through 527 or (resid 528 through 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 543 or (resid 544 and (name N or name CA o \ r name C or name O or name CB )) or resid 545 through 620 or resid 640 through 8 \ 11 or resid 815 through 1140 or resid 1201 through 1207)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 81 or re \ sid 83 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA o \ r name C or name O or name CB )) or resid 101 through 104 or (resid 105 and (nam \ e N or name CA or name C or name O or name CB )) or resid 106 through 139 or (re \ sid 140 through 141 and (name N or name CA or name C or name O or name CB )) or \ resid 142 through 155 or (resid 156 and (name N or name CA or name C or name O o \ r name CB )) or resid 157 through 158 or (resid 159 and (name N or name CA or na \ me C or name O or name CB )) or resid 165 through 199 or (resid 200 and (name N \ or name CA or name C or name O or name CB )) or resid 201 through 243 or resid 2 \ 64 through 331 or (resid 332 through 333 and (name N or name CA or name C or nam \ e O or name CB )) or resid 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB )) or resid 336 through 343 or resid 355 through 402 or (resi \ d 403 and (name N or name CA or name C or name O or name CB )) or resid 404 thro \ ugh 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) o \ r resid 442 or resid 455 or (resid 457 and (name N or name CA or name C or name \ O or name CB )) or resid 458 or resid 491 through 500 or resid 503 through 504 o \ r (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 06 through 543 or (resid 544 and (name N or name CA or name C or name O or name \ CB )) or resid 545 through 620 or resid 640 through 672 or resid 687 through 811 \ or resid 815 through 1140 or resid 1201 through 1207)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'N' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'Q' selection = chain 'h' } ncs_group { reference = (chain 'V' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) } 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 106 5.16 5 C 15304 2.51 5 N 3942 2.21 5 O 4700 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.360 Check model and map are aligned: 0.350 Process input model: 63.500 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.010 0.232 24570 Z= 0.685 Angle : 1.156 20.755 33483 Z= 0.684 Chirality : 0.066 0.993 4035 Planarity : 0.010 0.288 4250 Dihedral : 15.310 89.641 8659 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 47.45 Ramachandran Plot: Outliers : 1.13 % Allowed : 21.36 % Favored : 77.51 % Rotamer Outliers : 2.39 % 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: -5.89 (0.11), residues: 3006 helix: -3.38 (0.14), residues: 625 sheet: -3.19 (0.22), residues: 384 loop : -4.58 (0.10), residues: 1997 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 612 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 656 average time/residue: 0.3696 time to fit residues: 376.5541 Evaluate side-chains 532 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 500 time to evaluate : 2.951 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.2557 time to fit residues: 18.2733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 145 optimal weight: 50.0000 chunk 177 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 125 ASN A 134 GLN A 148 ASN A 188 ASN A 207 HIS A 613 GLN A 641 ASN A 655 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 953 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 49 HIS ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 317 ASN B 542 ASN B 564 GLN B 607 GLN B 613 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 949 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 955 ASN B 992 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 644 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.140 24570 Z= 0.302 Angle : 0.820 12.201 33483 Z= 0.440 Chirality : 0.053 0.698 4035 Planarity : 0.006 0.071 4250 Dihedral : 7.307 87.948 3604 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.11 % Favored : 85.76 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % 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: -4.75 (0.12), residues: 3006 helix: -1.86 (0.18), residues: 626 sheet: -2.79 (0.24), residues: 384 loop : -3.96 (0.11), residues: 1996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 646 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 653 average time/residue: 0.3568 time to fit residues: 366.5004 Evaluate side-chains 543 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 540 time to evaluate : 3.041 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2124 time to fit residues: 5.3590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 247 optimal weight: 0.0370 chunk 275 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1088 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 448 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 925 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C 992 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 24570 Z= 0.242 Angle : 0.755 11.323 33483 Z= 0.401 Chirality : 0.050 0.459 4035 Planarity : 0.005 0.072 4250 Dihedral : 7.027 105.684 3604 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.94 % Favored : 85.93 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % 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: -4.09 (0.13), residues: 3006 helix: -1.00 (0.19), residues: 634 sheet: -2.45 (0.24), residues: 404 loop : -3.62 (0.11), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 640 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 646 average time/residue: 0.3386 time to fit residues: 346.7306 Evaluate side-chains 545 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 543 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1677 time to fit residues: 3.7457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 658 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1054 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 24570 Z= 0.301 Angle : 0.761 11.936 33483 Z= 0.408 Chirality : 0.050 0.581 4035 Planarity : 0.005 0.069 4250 Dihedral : 7.013 105.874 3604 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.60 % Favored : 85.26 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % 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: -3.87 (0.13), residues: 3006 helix: -0.70 (0.19), residues: 620 sheet: -2.47 (0.24), residues: 413 loop : -3.47 (0.12), residues: 1973 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 625 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 628 average time/residue: 0.3652 time to fit residues: 368.1505 Evaluate side-chains 522 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 521 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2295 time to fit residues: 3.8746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 219 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 251 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1058 HIS A1064 HIS B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 925 ASN C 957 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1054 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 24570 Z= 0.252 Angle : 0.727 10.240 33483 Z= 0.388 Chirality : 0.049 0.483 4035 Planarity : 0.005 0.076 4250 Dihedral : 6.833 106.006 3604 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.81 % Favored : 86.09 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % 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: -3.65 (0.14), residues: 3006 helix: -0.46 (0.20), residues: 626 sheet: -2.35 (0.24), residues: 387 loop : -3.34 (0.12), residues: 1993 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 612 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 614 average time/residue: 0.3482 time to fit residues: 340.7026 Evaluate side-chains 521 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2165 time to fit residues: 4.1595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 20.0000 chunk 265 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 72 optimal weight: 0.0570 chunk 295 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 overall best weight: 4.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 87 ASN B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 24570 Z= 0.323 Angle : 0.774 11.615 33483 Z= 0.414 Chirality : 0.051 0.636 4035 Planarity : 0.005 0.072 4250 Dihedral : 6.959 105.752 3604 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.24 % Favored : 84.66 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % 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: -3.71 (0.14), residues: 3006 helix: -0.60 (0.20), residues: 626 sheet: -2.31 (0.24), residues: 380 loop : -3.37 (0.12), residues: 2000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 604 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 605 average time/residue: 0.3490 time to fit residues: 338.0623 Evaluate side-chains 515 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 5.9990 chunk 33 optimal weight: 0.0040 chunk 168 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 135 optimal weight: 0.0270 overall best weight: 0.7452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 953 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1054 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 24570 Z= 0.210 Angle : 0.717 9.824 33483 Z= 0.380 Chirality : 0.049 0.492 4035 Planarity : 0.005 0.069 4250 Dihedral : 6.575 106.411 3604 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.84 % Favored : 88.09 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % 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: -3.36 (0.14), residues: 3006 helix: -0.09 (0.20), residues: 613 sheet: -2.03 (0.25), residues: 416 loop : -3.21 (0.12), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 633 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 635 average time/residue: 0.3643 time to fit residues: 368.5491 Evaluate side-chains 521 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2137 time to fit residues: 4.0845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 925 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 24570 Z= 0.247 Angle : 0.719 9.556 33483 Z= 0.385 Chirality : 0.049 0.480 4035 Planarity : 0.005 0.102 4250 Dihedral : 6.521 106.611 3604 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.74 % Favored : 87.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: -3.27 (0.14), residues: 3006 helix: -0.07 (0.20), residues: 621 sheet: -1.96 (0.26), residues: 381 loop : -3.14 (0.12), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 0.3592 time to fit residues: 348.3462 Evaluate side-chains 505 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 chunk 273 optimal weight: 0.0570 chunk 164 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1064 HIS ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 24570 Z= 0.211 Angle : 0.708 9.216 33483 Z= 0.377 Chirality : 0.049 0.443 4035 Planarity : 0.005 0.091 4250 Dihedral : 6.369 106.821 3604 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.98 % Favored : 87.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: -3.10 (0.14), residues: 3006 helix: 0.11 (0.21), residues: 621 sheet: -1.75 (0.26), residues: 389 loop : -3.07 (0.12), residues: 1996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.3699 time to fit residues: 367.5139 Evaluate side-chains 513 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 1.9990 chunk 289 optimal weight: 0.0970 chunk 176 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 24570 Z= 0.206 Angle : 0.712 10.773 33483 Z= 0.378 Chirality : 0.048 0.420 4035 Planarity : 0.005 0.081 4250 Dihedral : 6.272 107.027 3604 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.44 % Favored : 88.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: -2.98 (0.14), residues: 3006 helix: 0.12 (0.20), residues: 627 sheet: -1.69 (0.26), residues: 394 loop : -2.97 (0.13), residues: 1985 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.3670 time to fit residues: 354.2247 Evaluate side-chains 518 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 2.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1064 HIS B 87 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C 978 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.174204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143208 restraints weight = 56530.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147237 restraints weight = 34504.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149877 restraints weight = 23479.913| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 24570 Z= 0.285 Angle : 0.745 10.292 33483 Z= 0.401 Chirality : 0.049 0.467 4035 Planarity : 0.005 0.083 4250 Dihedral : 6.432 106.881 3604 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.87 % Favored : 87.06 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % 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: -3.11 (0.14), residues: 3006 helix: 0.03 (0.20), residues: 617 sheet: -1.90 (0.26), residues: 377 loop : -3.00 (0.12), residues: 2012 =============================================================================== Job complete usr+sys time: 6188.50 seconds wall clock time: 114 minutes 44.74 seconds (6884.74 seconds total)