Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 21:11:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wor_32656/10_2023/7wor_32656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wor_32656/10_2023/7wor_32656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wor_32656/10_2023/7wor_32656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wor_32656/10_2023/7wor_32656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wor_32656/10_2023/7wor_32656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wor_32656/10_2023/7wor_32656.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 18904 2.51 5 N 4911 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ARG 223": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 29670 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.23, per 1000 atoms: 0.51 Number of scatterers: 29670 At special positions: 0 Unit cell: (146.832, 161.728, 203.224, 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 134 16.00 O 5721 8.00 N 4911 7.00 C 18904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 10.91 Conformation dependent library (CDL) restraints added in 4.2 seconds 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 57 sheets defined 18.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.054A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.815A pdb=" N GLY A 447 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.545A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.814A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.084A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.544A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.537A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.604A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.093A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.984A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.102A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.701A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.563A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 781 removed outlier: 3.564A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.659A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.337A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.548A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.862A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 336 through 341 removed outlier: 4.122A pdb=" N ASP C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.941A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.590A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.872A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 780 removed outlier: 3.657A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.631A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.605A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.427A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.670A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.902A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.670A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.676A pdb=" N ARG B 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.359A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.707A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.557A pdb=" N VAL A 191 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.492A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.955A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.783A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.525A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.762A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.633A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 229 removed outlier: 3.702A pdb=" N LEU B 226 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.686A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.522A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.736A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 718 removed outlier: 7.066A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.113A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.808A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.935A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 192 through 194 removed outlier: 7.495A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.999A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.524A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.716A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.782A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.812A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.126A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AF4, first strand: chain 'D' and resid 172 through 177 removed outlier: 6.088A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 177 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 160 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AF6, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.006A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.006A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.557A pdb=" N SER E 131 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.648A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.138A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 64 through 69 removed outlier: 5.373A pdb=" N SER F 65 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 172 through 176 removed outlier: 6.082A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.90 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7896 1.33 - 1.45: 5888 1.45 - 1.57: 16409 1.57 - 1.69: 0 1.69 - 1.82: 172 Bond restraints: 30365 Sorted by residual: bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.23e-02 6.61e+03 4.74e+01 bond pdb=" CA ASN C1134 " pdb=" C ASN C1134 " ideal model delta sigma weight residual 1.523 1.459 0.065 1.19e-02 7.06e+03 2.95e+01 bond pdb=" CA TYR B 707 " pdb=" C TYR B 707 " ideal model delta sigma weight residual 1.525 1.465 0.060 1.28e-02 6.10e+03 2.17e+01 bond pdb=" CA ASN B 801 " pdb=" C ASN B 801 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.08e-02 8.57e+03 1.87e+01 bond pdb=" CA ASN C 280 " pdb=" C ASN C 280 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.34e-02 5.57e+03 1.67e+01 ... (remaining 30360 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 967 107.15 - 113.85: 16715 113.85 - 120.56: 11244 120.56 - 127.27: 12126 127.27 - 133.97: 277 Bond angle restraints: 41329 Sorted by residual: angle pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" C ASN A 616 " ideal model delta sigma weight residual 112.93 107.19 5.74 1.12e+00 7.97e-01 2.63e+01 angle pdb=" N GLU A 281 " pdb=" CA GLU A 281 " pdb=" C GLU A 281 " ideal model delta sigma weight residual 111.71 106.00 5.71 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 109.24 101.31 7.93 1.63e+00 3.76e-01 2.37e+01 angle pdb=" N ALA C 27 " pdb=" CA ALA C 27 " pdb=" C ALA C 27 " ideal model delta sigma weight residual 110.80 100.44 10.36 2.13e+00 2.20e-01 2.37e+01 angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.53 108.78 4.75 9.80e-01 1.04e+00 2.35e+01 ... (remaining 41324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 17010 16.86 - 33.72: 686 33.72 - 50.58: 114 50.58 - 67.45: 29 67.45 - 84.31: 4 Dihedral angle restraints: 17843 sinusoidal: 6852 harmonic: 10991 Sorted by residual: dihedral pdb=" CA ALA C 27 " pdb=" C ALA C 27 " pdb=" N TYR C 28 " pdb=" CA TYR C 28 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR C 28 " pdb=" C TYR C 28 " pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS B 336 " pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " ideal model delta sinusoidal sigma weight residual 79.00 20.41 58.59 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 17840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 4707 0.294 - 0.588: 2 0.588 - 0.881: 1 0.881 - 1.175: 0 1.175 - 1.469: 1 Chirality restraints: 4711 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.39e+01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.43e+00 ... (remaining 4708 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " 0.357 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG C1304 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1307 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.088 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1308 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " -0.178 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3132 2.75 - 3.29: 29561 3.29 - 3.83: 48424 3.83 - 4.36: 55090 4.36 - 4.90: 95448 Nonbonded interactions: 231655 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.216 2.440 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.219 2.440 nonbonded pdb=" OG1 THR C 719 " pdb=" O VAL C1068 " model vdw 2.236 2.440 nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR B 719 " pdb=" O VAL B1068 " model vdw 2.240 2.440 ... (remaining 231650 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 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'C' and (resid 26 through 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.400 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: 8.220 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 74.380 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.003 0.085 30365 Z= 0.203 Angle : 0.526 10.359 41329 Z= 0.292 Chirality : 0.049 1.469 4711 Planarity : 0.014 0.307 5333 Dihedral : 9.190 84.306 10673 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 5.34 % Allowed : 8.31 % Favored : 86.35 % 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: -4.04 (0.11), residues: 3739 helix: -0.58 (0.19), residues: 658 sheet: -2.46 (0.18), residues: 630 loop : -3.61 (0.10), residues: 2451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 628 time to evaluate : 3.388 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 outliers start: 173 outliers final: 60 residues processed: 773 average time/residue: 0.4237 time to fit residues: 511.1570 Evaluate side-chains 533 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 473 time to evaluate : 2.933 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 2 residues processed: 60 average time/residue: 0.3376 time to fit residues: 38.7219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 20.0000 chunk 285 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 342 optimal weight: 30.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 173 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 422 ASN A 540 ASN A 564 GLN A 613 GLN A 784 GLN A 853 GLN A 901 GLN A 955 ASN A1005 GLN A1011 GLN A1048 HIS A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 173 GLN B 181 GLN B 245 HIS B 321 GLN B 354 ASN B 370 ASN B 388 ASN B 448 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 895 GLN B 901 GLN B 914 ASN B 926 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1054 GLN B1119 ASN ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 99 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 205 HIS C 218 GLN C 271 GLN C 321 GLN C 354 ASN C 370 ASN C 388 ASN C 409 GLN C 422 ASN C 448 ASN C 477 ASN C 540 ASN C 580 GLN C 613 GLN C 641 ASN C 784 GLN C 853 GLN C 872 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 949 GLN C 953 ASN C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1106 GLN C1119 ASN ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 165 GLN D 202 ASN E 6 GLN E 16 GLN E 80 GLN E 97 ASN E 127 GLN E 137 GLN E 201 ASN E 206 GLN F 39 GLN F 40 GLN F 165 GLN F 202 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30365 Z= 0.282 Angle : 0.637 11.700 41329 Z= 0.319 Chirality : 0.047 0.521 4711 Planarity : 0.004 0.049 5333 Dihedral : 3.573 37.901 4086 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.21 % Allowed : 15.10 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.12), residues: 3739 helix: 0.30 (0.21), residues: 677 sheet: -1.98 (0.19), residues: 637 loop : -3.24 (0.10), residues: 2425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 495 time to evaluate : 3.138 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 outliers start: 104 outliers final: 44 residues processed: 563 average time/residue: 0.4120 time to fit residues: 369.3305 Evaluate side-chains 502 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 458 time to evaluate : 3.152 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.2832 time to fit residues: 27.2082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 284 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 342 optimal weight: 30.0000 chunk 370 optimal weight: 0.6980 chunk 305 optimal weight: 0.0980 chunk 340 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 935 GLN A 955 ASN A1005 GLN A1048 HIS A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 644 GLN B 926 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 477 ASN C 487 ASN C 563 GLN C 613 GLN C 658 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C1011 GLN C1125 ASN E 6 GLN E 35 ASN E 127 GLN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30365 Z= 0.183 Angle : 0.583 13.878 41329 Z= 0.286 Chirality : 0.045 0.447 4711 Planarity : 0.004 0.050 5333 Dihedral : 3.593 39.082 4086 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.50 % Allowed : 17.04 % Favored : 80.46 % 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: -3.02 (0.13), residues: 3739 helix: 0.61 (0.21), residues: 679 sheet: -1.95 (0.19), residues: 609 loop : -3.01 (0.11), residues: 2451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 465 time to evaluate : 3.357 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 outliers start: 81 outliers final: 39 residues processed: 517 average time/residue: 0.4261 time to fit residues: 349.8067 Evaluate side-chains 473 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 434 time to evaluate : 3.137 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.2692 time to fit residues: 24.2141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 50.0000 chunk 257 optimal weight: 0.0770 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 364 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 804 GLN C 81 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C 955 ASN E 35 ASN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30365 Z= 0.221 Angle : 0.596 14.400 41329 Z= 0.293 Chirality : 0.045 0.468 4711 Planarity : 0.004 0.057 5333 Dihedral : 3.782 39.671 4086 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.44 % Allowed : 17.88 % Favored : 79.69 % 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: -2.80 (0.13), residues: 3739 helix: 0.74 (0.21), residues: 678 sheet: -1.64 (0.19), residues: 676 loop : -2.91 (0.11), residues: 2385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 458 time to evaluate : 3.517 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 outliers start: 79 outliers final: 36 residues processed: 508 average time/residue: 0.4239 time to fit residues: 342.3403 Evaluate side-chains 474 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 438 time to evaluate : 3.213 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 0.2929 time to fit residues: 23.6338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 271 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 641 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 448 ASN B 607 GLN B 641 ASN B1106 GLN C 448 ASN C 949 GLN C 953 ASN C1011 GLN D 39 GLN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 30365 Z= 0.496 Angle : 0.741 12.178 41329 Z= 0.374 Chirality : 0.050 0.447 4711 Planarity : 0.005 0.082 5333 Dihedral : 4.567 43.184 4086 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 2.66 % Allowed : 18.46 % Favored : 78.88 % 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: -3.01 (0.13), residues: 3739 helix: 0.36 (0.21), residues: 669 sheet: -1.84 (0.18), residues: 709 loop : -2.94 (0.11), residues: 2361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 479 time to evaluate : 3.183 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 outliers start: 86 outliers final: 41 residues processed: 529 average time/residue: 0.4143 time to fit residues: 347.9825 Evaluate side-chains 484 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 443 time to evaluate : 3.339 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.2729 time to fit residues: 25.9039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 8.9990 chunk 328 optimal weight: 30.0000 chunk 72 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 364 optimal weight: 40.0000 chunk 302 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1002 GLN B1010 GLN C 641 ASN C 949 GLN C 953 ASN C 955 ASN C1011 GLN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30365 Z= 0.212 Angle : 0.626 10.927 41329 Z= 0.313 Chirality : 0.046 0.411 4711 Planarity : 0.004 0.054 5333 Dihedral : 4.201 39.892 4086 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.13 % Allowed : 19.60 % Favored : 78.26 % 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: -2.70 (0.13), residues: 3739 helix: 0.74 (0.21), residues: 679 sheet: -1.69 (0.18), residues: 722 loop : -2.78 (0.12), residues: 2338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 449 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 31 residues processed: 492 average time/residue: 0.4314 time to fit residues: 338.8745 Evaluate side-chains 457 residues out of total 3290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 426 time to evaluate : 3.157 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2902 time to fit residues: 20.8048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.0772 > 50: distance: 19 - 106: 16.521 distance: 85 - 91: 3.271 distance: 92 - 93: 6.754 distance: 93 - 94: 11.168 distance: 93 - 95: 27.530 distance: 95 - 96: 19.750 distance: 96 - 97: 26.726 distance: 96 - 99: 8.911 distance: 97 - 98: 18.573 distance: 97 - 103: 10.070 distance: 99 - 100: 21.963 distance: 99 - 101: 28.764 distance: 100 - 102: 15.308 distance: 103 - 104: 8.621 distance: 104 - 105: 10.273 distance: 104 - 107: 12.586 distance: 105 - 106: 15.669 distance: 105 - 110: 21.957 distance: 107 - 108: 18.111 distance: 107 - 109: 11.879 distance: 110 - 111: 4.888 distance: 111 - 112: 12.417 distance: 111 - 114: 12.211 distance: 112 - 113: 10.649 distance: 112 - 118: 7.109 distance: 114 - 115: 15.957 distance: 115 - 116: 8.611 distance: 115 - 117: 6.222 distance: 117 - 186: 10.177 distance: 118 - 119: 5.147 distance: 119 - 120: 4.411 distance: 119 - 122: 10.924 distance: 120 - 121: 9.016 distance: 120 - 126: 4.381 distance: 122 - 123: 18.545 distance: 123 - 124: 19.132 distance: 123 - 125: 28.821 distance: 126 - 127: 9.174 distance: 127 - 128: 8.108 distance: 127 - 130: 12.682 distance: 128 - 129: 7.603 distance: 128 - 133: 4.495 distance: 130 - 131: 23.135 distance: 130 - 132: 31.883 distance: 133 - 134: 3.984 distance: 134 - 135: 4.851 distance: 134 - 137: 3.559 distance: 135 - 136: 3.671 distance: 135 - 140: 6.898 distance: 137 - 138: 14.347 distance: 137 - 139: 13.813 distance: 140 - 141: 5.697 distance: 141 - 142: 15.835 distance: 141 - 144: 17.726 distance: 142 - 143: 22.666 distance: 142 - 152: 21.128 distance: 144 - 145: 9.730 distance: 145 - 146: 17.387 distance: 145 - 147: 19.485 distance: 146 - 148: 8.620 distance: 147 - 149: 3.374 distance: 148 - 150: 17.197 distance: 149 - 150: 21.777 distance: 150 - 151: 8.762 distance: 152 - 153: 21.598 distance: 153 - 154: 21.636 distance: 153 - 156: 6.883 distance: 154 - 155: 10.506 distance: 154 - 160: 5.434 distance: 156 - 157: 15.299 distance: 157 - 158: 3.865 distance: 157 - 159: 21.302 distance: 160 - 161: 6.128 distance: 160 - 166: 11.399 distance: 161 - 162: 3.277 distance: 161 - 164: 11.126 distance: 162 - 163: 15.980 distance: 162 - 167: 7.130 distance: 164 - 165: 12.902 distance: 165 - 166: 17.663