Starting phenix.real_space_refine on Mon Nov 20 06:23:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whk_32503/11_2023/7whk_32503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whk_32503/11_2023/7whk_32503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whk_32503/11_2023/7whk_32503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whk_32503/11_2023/7whk_32503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whk_32503/11_2023/7whk_32503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whk_32503/11_2023/7whk_32503.pdb" } resolution = 3.01 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= 0.022 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 142 5.16 5 C 18606 2.51 5 N 4806 2.21 5 O 5596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 287": "OD1" <-> "OD2" 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 "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" 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 "C ARG 346": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" 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 ARG 847": "NH1" <-> "NH2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "G ARG 56": "NH1" <-> "NH2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 29150 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8101 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 981} 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: 7999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 7999 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 970} 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: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8129 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 984} 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: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.75, per 1000 atoms: 0.51 Number of scatterers: 29150 At special positions: 0 Unit cell: (147.896, 171.304, 198.968, 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 142 16.00 O 5596 8.00 N 4806 7.00 C 18606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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 538 " - pdb=" SG CYS B 590 " 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 15 " - pdb=" SG CYS C 136 " 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " 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 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 709 " Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 5.0 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6900 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 64 sheets defined 19.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.639A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.642A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 780 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.847A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.634A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.074A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.573A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.154A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.516A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.564A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.526A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.551A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.676A pdb=" N GLN B 755 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 756 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.786A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 853 removed outlier: 3.625A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.184A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.527A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.944A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.588A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.085A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.855A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.859A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.860A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.613A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.677A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 854 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.216A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.682A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 removed outlier: 3.667A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.460A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.525A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 90' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.692A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.943A pdb=" N THR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.045A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG A 188 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.575A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 128 removed outlier: 3.844A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.943A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.598A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 7.779A pdb=" N VAL A 433 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE A 377 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.643A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.905A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.211A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.777A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.703A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.281A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.281A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.578A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.638A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.995A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.854A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.691A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.648A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.814A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.322A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.954A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.465A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.628A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.760A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.760A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.744A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.898A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 542 removed outlier: 3.609A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.004A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.830A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.912A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET D 83 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.922A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP D 36 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.573A pdb=" N SER D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.476A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG5, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.663A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.953A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.817A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AH1, first strand: chain 'H' and resid 49 through 51 925 hydrogen bonds defined for protein. 2478 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: 12.14 Time building geometry restraints manager: 11.43 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: 6270 1.33 - 1.45: 7201 1.45 - 1.57: 16174 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 29833 Sorted by residual: bond pdb=" CA LYS A 300 " pdb=" C LYS A 300 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.29e-02 6.01e+03 2.36e+01 bond pdb=" CA ASN C 331 " pdb=" C ASN C 331 " ideal model delta sigma weight residual 1.524 1.467 0.056 1.31e-02 5.83e+03 1.83e+01 bond pdb=" CA SER A 297 " pdb=" C SER A 297 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.39e-02 5.18e+03 1.69e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.33e-02 5.65e+03 1.68e+01 bond pdb=" CA CYS A 301 " pdb=" C CYS A 301 " ideal model delta sigma weight residual 1.522 1.464 0.057 1.40e-02 5.10e+03 1.66e+01 ... (remaining 29828 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 980 107.14 - 113.85: 16383 113.85 - 120.56: 11309 120.56 - 127.27: 11674 127.27 - 133.98: 265 Bond angle restraints: 40611 Sorted by residual: angle pdb=" N ALA A 123 " pdb=" CA ALA A 123 " pdb=" C ALA A 123 " ideal model delta sigma weight residual 114.56 106.27 8.29 1.27e+00 6.20e-01 4.27e+01 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 113.18 120.76 -7.58 1.21e+00 6.83e-01 3.92e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.31 114.80 5.51 9.80e-01 1.04e+00 3.16e+01 angle pdb=" N GLU A 298 " pdb=" CA GLU A 298 " pdb=" C GLU A 298 " ideal model delta sigma weight residual 111.36 105.75 5.61 1.09e+00 8.42e-01 2.65e+01 angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 120.87 128.05 -7.18 1.42e+00 4.96e-01 2.56e+01 ... (remaining 40606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 16508 17.89 - 35.78: 720 35.78 - 53.67: 209 53.67 - 71.56: 60 71.56 - 89.44: 17 Dihedral angle restraints: 17514 sinusoidal: 6764 harmonic: 10750 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.19 -80.19 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" C ASN A 343 " pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " ideal model delta harmonic sigma weight residual -122.60 -110.16 -12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -121.01 35.01 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 17511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 4641 0.241 - 0.482: 12 0.482 - 0.722: 2 0.722 - 0.963: 0 0.963 - 1.204: 1 Chirality restraints: 4656 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.62e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.90e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 4653 not shown) Planarity restraints: 5241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.340 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A1306 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.320 2.00e-02 2.50e+03 2.69e-01 9.03e+02 pdb=" C7 NAG C1310 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.194 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.303 2.00e-02 2.50e+03 2.56e-01 8.16e+02 pdb=" C7 NAG C1304 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.441 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.032 2.00e-02 2.50e+03 ... (remaining 5238 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2786 2.75 - 3.28: 28075 3.28 - 3.82: 47948 3.82 - 4.36: 56113 4.36 - 4.90: 96411 Nonbonded interactions: 231333 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.208 2.440 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.231 2.440 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.235 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.266 2.440 ... (remaining 231328 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 177 or resid 182 through 244 or resid 262 throu \ gh 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 26 through 827 or resid 848 through 1147 or resid 1301 thr \ ough 1308)) selection = (chain 'C' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 848 through 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and resid 1 through 116) selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.070 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 74.470 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.004 0.063 29833 Z= 0.261 Angle : 0.698 10.788 40611 Z= 0.425 Chirality : 0.054 1.204 4656 Planarity : 0.013 0.290 5213 Dihedral : 11.563 89.444 10476 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.58 % Favored : 94.15 % Rotamer: Outliers : 6.30 % Allowed : 6.42 % Favored : 87.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 3639 helix: -0.18 (0.20), residues: 609 sheet: -2.12 (0.16), residues: 883 loop : -3.16 (0.11), residues: 2147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 685 time to evaluate : 2.939 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: 200 outliers final: 49 residues processed: 830 average time/residue: 0.4275 time to fit residues: 553.5380 Evaluate side-chains 576 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 527 time to evaluate : 3.174 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 2 residues processed: 49 average time/residue: 0.3021 time to fit residues: 30.6562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 1.9990 chunk 276 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 331 optimal weight: 2.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 239 GLN A 314 GLN A 388 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 414 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 755 GLN A 762 GLN A 784 GLN A 907 ASN A1002 GLN A1048 HIS A1119 ASN B 205 HIS B 239 GLN B 271 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 641 ASN B 751 ASN B 784 GLN B 907 ASN B 954 HIS B1002 GLN B1048 HIS B1101 HIS B1106 GLN C 23 GLN C 66 HIS C 115 GLN C 173 GLN C 343 ASN C 394 ASN C 409 GLN C 417 ASN C 540 ASN C 580 GLN C 641 ASN C 784 GLN C 901 GLN C 925 ASN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1048 HIS C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN E 81 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 13 GLN G 98 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29833 Z= 0.201 Angle : 0.577 9.017 40611 Z= 0.293 Chirality : 0.044 0.245 4656 Planarity : 0.005 0.059 5213 Dihedral : 3.698 21.139 3984 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.08 % Allowed : 13.22 % Favored : 83.70 % 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: -2.62 (0.13), residues: 3639 helix: 0.91 (0.22), residues: 625 sheet: -1.68 (0.16), residues: 868 loop : -2.72 (0.11), residues: 2146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 525 time to evaluate : 2.883 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: 98 outliers final: 45 residues processed: 588 average time/residue: 0.4162 time to fit residues: 382.7858 Evaluate side-chains 529 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 484 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2626 time to fit residues: 26.6048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 30.0000 chunk 358 optimal weight: 0.0870 chunk 295 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 644 GLN A 762 GLN A 907 ASN A 955 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN B1119 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 29833 Z= 0.363 Angle : 0.645 12.608 40611 Z= 0.326 Chirality : 0.047 0.415 4656 Planarity : 0.005 0.057 5213 Dihedral : 4.179 25.158 3984 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.64 % Allowed : 14.64 % Favored : 82.72 % 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: -2.20 (0.13), residues: 3639 helix: 1.08 (0.21), residues: 636 sheet: -1.32 (0.16), residues: 891 loop : -2.45 (0.12), residues: 2112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 525 time to evaluate : 3.081 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 outliers start: 84 outliers final: 46 residues processed: 582 average time/residue: 0.4437 time to fit residues: 403.1047 Evaluate side-chains 525 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 479 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2711 time to fit residues: 28.2283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 10.0000 chunk 249 optimal weight: 0.0040 chunk 172 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 333 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 556 ASN A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 29833 Z= 0.307 Angle : 0.622 11.986 40611 Z= 0.313 Chirality : 0.046 0.304 4656 Planarity : 0.004 0.062 5213 Dihedral : 4.257 26.566 3984 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.98 % Allowed : 16.08 % Favored : 81.93 % 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: -1.94 (0.13), residues: 3639 helix: 1.19 (0.21), residues: 654 sheet: -1.19 (0.16), residues: 917 loop : -2.26 (0.12), residues: 2068 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 504 time to evaluate : 3.188 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 outliers start: 63 outliers final: 35 residues processed: 547 average time/residue: 0.4537 time to fit residues: 386.6927 Evaluate side-chains 519 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 484 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2802 time to fit residues: 22.8280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 301 optimal weight: 0.5980 chunk 243 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 186 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A1106 GLN B 30 ASN B 121 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29833 Z= 0.292 Angle : 0.618 13.359 40611 Z= 0.313 Chirality : 0.046 0.352 4656 Planarity : 0.004 0.061 5213 Dihedral : 4.299 25.740 3984 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.79 % Allowed : 16.65 % Favored : 81.55 % 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: -1.78 (0.13), residues: 3639 helix: 1.39 (0.21), residues: 642 sheet: -1.12 (0.16), residues: 925 loop : -2.15 (0.12), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 501 time to evaluate : 3.390 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 outliers start: 57 outliers final: 28 residues processed: 542 average time/residue: 0.4593 time to fit residues: 386.8978 Evaluate side-chains 507 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 479 time to evaluate : 3.037 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2684 time to fit residues: 18.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 353 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN B 613 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 29833 Z= 0.379 Angle : 0.665 13.549 40611 Z= 0.338 Chirality : 0.047 0.423 4656 Planarity : 0.005 0.062 5213 Dihedral : 4.554 27.317 3984 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.79 % Allowed : 17.09 % Favored : 81.11 % 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: -1.67 (0.13), residues: 3639 helix: 1.33 (0.21), residues: 655 sheet: -1.02 (0.16), residues: 917 loop : -2.04 (0.13), residues: 2067 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 506 time to evaluate : 3.409 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 outliers start: 57 outliers final: 28 residues processed: 538 average time/residue: 0.4695 time to fit residues: 395.4832 Evaluate side-chains 517 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 489 time to evaluate : 2.830 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2921 time to fit residues: 19.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 351 optimal weight: 0.0010 chunk 220 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 239 GLN B 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29833 Z= 0.198 Angle : 0.610 11.932 40611 Z= 0.310 Chirality : 0.045 0.560 4656 Planarity : 0.004 0.060 5213 Dihedral : 4.324 25.793 3984 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.10 % Allowed : 18.19 % Favored : 80.71 % 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: -1.47 (0.14), residues: 3639 helix: 1.62 (0.21), residues: 650 sheet: -0.95 (0.16), residues: 930 loop : -1.93 (0.13), residues: 2059 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 494 time to evaluate : 3.494 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 outliers start: 35 outliers final: 16 residues processed: 513 average time/residue: 0.4696 time to fit residues: 371.8314 Evaluate side-chains 492 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 476 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2781 time to fit residues: 12.9461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 223 optimal weight: 0.4980 chunk 239 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 907 ASN C 872 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29833 Z= 0.251 Angle : 0.641 14.157 40611 Z= 0.324 Chirality : 0.046 0.479 4656 Planarity : 0.004 0.059 5213 Dihedral : 4.384 34.302 3984 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 1.10 % Allowed : 18.76 % Favored : 80.14 % 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: -1.39 (0.14), residues: 3639 helix: 1.57 (0.21), residues: 656 sheet: -0.80 (0.16), residues: 924 loop : -1.90 (0.13), residues: 2059 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 478 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 498 average time/residue: 0.4633 time to fit residues: 359.5155 Evaluate side-chains 492 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 471 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2722 time to fit residues: 14.8333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 7.9990 chunk 337 optimal weight: 30.0000 chunk 307 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 336 optimal weight: 20.0000 chunk 197 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29833 Z= 0.278 Angle : 0.664 13.534 40611 Z= 0.335 Chirality : 0.046 0.427 4656 Planarity : 0.004 0.059 5213 Dihedral : 4.441 31.481 3984 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.95 % Favored : 93.02 % Rotamer: Outliers : 0.54 % Allowed : 19.26 % Favored : 80.20 % 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: -1.34 (0.14), residues: 3639 helix: 1.60 (0.21), residues: 656 sheet: -0.75 (0.16), residues: 932 loop : -1.87 (0.13), residues: 2051 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 485 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 495 average time/residue: 0.4698 time to fit residues: 358.9436 Evaluate side-chains 490 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 483 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2704 time to fit residues: 8.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 346 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 115 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.178 29833 Z= 0.690 Angle : 0.833 13.919 40611 Z= 0.423 Chirality : 0.054 0.434 4656 Planarity : 0.005 0.063 5213 Dihedral : 5.171 35.575 3984 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.23 % Favored : 90.68 % Rotamer: Outliers : 0.57 % Allowed : 19.64 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.69 (0.13), residues: 3639 helix: 1.01 (0.21), residues: 659 sheet: -0.97 (0.16), residues: 899 loop : -1.98 (0.13), residues: 2081 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 510 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 517 average time/residue: 0.4628 time to fit residues: 369.4071 Evaluate side-chains 505 residues out of total 3228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 491 time to evaluate : 2.955 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2924 time to fit residues: 11.7167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 308 optimal weight: 0.0770 chunk 88 optimal weight: 0.6980 chunk 266 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 290 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 297 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 239 GLN C 115 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.161931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121680 restraints weight = 48050.442| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.59 r_work: 0.3396 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29833 Z= 0.205 Angle : 0.673 12.690 40611 Z= 0.341 Chirality : 0.046 0.388 4656 Planarity : 0.005 0.062 5213 Dihedral : 4.690 29.517 3984 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 0.28 % Allowed : 20.52 % Favored : 79.19 % 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: -1.41 (0.14), residues: 3639 helix: 1.50 (0.21), residues: 658 sheet: -0.87 (0.16), residues: 916 loop : -1.86 (0.13), residues: 2065 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8523.74 seconds wall clock time: 153 minutes 53.03 seconds (9233.03 seconds total)