Starting phenix.real_space_refine on Thu Jun 26 18:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz4_26878/06_2025/7uz4_26878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz4_26878/06_2025/7uz4_26878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz4_26878/06_2025/7uz4_26878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz4_26878/06_2025/7uz4_26878.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz4_26878/06_2025/7uz4_26878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz4_26878/06_2025/7uz4_26878.cif" } resolution = 3.1 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= 0.000 sd= 0.027 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 135 5.16 5 C 19575 2.51 5 N 5037 2.21 5 O 6015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30762 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8247 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8247 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8247 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "P" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 17.74, per 1000 atoms: 0.58 Number of scatterers: 30762 At special positions: 0 Unit cell: (154.752, 165.568, 194.688, 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 135 16.00 O 6015 8.00 N 5037 7.00 C 19575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 122 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 234 " " NAG A1314 " - " ASN A 282 " " NAG A1315 " - " ASN A 801 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 343 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 122 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 234 " " NAG B1314 " - " ASN B 282 " " NAG B1315 " - " ASN B 801 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 234 " " NAG C1314 " - " ASN C 282 " " NAG C1315 " - " ASN C 801 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 7.95 Conformation dependent library (CDL) restraints added in 3.9 seconds 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 22.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.827A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.952A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.995A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.834A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.594A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.599A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.536A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.241A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.470A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.847A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.622A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.808A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.657A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.532A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.592A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.693A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.527A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.577A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.001A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.699A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.990A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.709A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.536A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.559A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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: 3.542A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.319A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.641A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.876A pdb=" N SER H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 85 Processing helix chain 'M' and resid 95 through 99 removed outlier: 3.535A pdb=" N ASP M 98 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER M 99 " --> pdb=" O SER M 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 95 through 99' Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.505A pdb=" N ASN P 36 " --> pdb=" O THR P 29 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR P 37 " --> pdb=" O PHE P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 37' Processing helix chain 'P' and resid 69 through 72 removed outlier: 4.298A pdb=" N LYS P 72 " --> pdb=" O GLN P 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 69 through 72' Processing helix chain 'P' and resid 82 through 85 Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'Q' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.356A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.940A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.340A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.938A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.216A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.517A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.529A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 removed outlier: 4.178A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 removed outlier: 4.178A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.772A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.531A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1047 through 1048 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.391A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.878A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.129A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.858A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.551A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.565A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.565A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) 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 473 through 474 removed outlier: 3.599A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.510A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.530A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.859A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.144A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.640A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.540A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.540A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.177A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 379 through 380 removed outlier: 3.534A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 379 through 380 removed outlier: 3.534A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.065A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.804A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.575A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.733A pdb=" N LYS H 24 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL H 19 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU H 91 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.088A pdb=" N TRP H 118 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG H 106 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN H 120 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS H 104 " --> pdb=" O GLN H 120 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET H 39 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.077A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.978A pdb=" N MET L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'L' and resid 51 through 52 removed outlier: 3.509A pdb=" N TYR L 42 " --> pdb=" O HIS L 103 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS L 103 " --> pdb=" O TYR L 42 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.647A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS M 40 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET M 39 " --> pdb=" O GLU M 55 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU M 55 " --> pdb=" O MET M 39 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS M 66 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 19 through 21 removed outlier: 3.866A pdb=" N VAL M 19 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU M 91 " --> pdb=" O VAL M 19 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.521A pdb=" N HIS N 103 " --> pdb=" O TYR N 42 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.894A pdb=" N VAL N 19 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR N 87 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR N 88 " --> pdb=" O SER N 79 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER N 79 " --> pdb=" O THR N 88 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AG8, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.651A pdb=" N THR P 125 " --> pdb=" O GLU P 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL P 42 " --> pdb=" O TYR P 103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS P 40 " --> pdb=" O ALA P 105 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG P 45 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU P 50 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS P 66 " --> pdb=" O GLU P 55 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.651A pdb=" N THR P 125 " --> pdb=" O GLU P 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR P 117 " --> pdb=" O ARG P 106 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 18 through 21 removed outlier: 3.651A pdb=" N LEU P 91 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR P 86 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.540A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR Q 90 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 50 through 54 removed outlier: 6.823A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR Q 117 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3057 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: 16.19 Time building geometry restraints manager: 9.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9771 1.34 - 1.47: 8121 1.47 - 1.59: 13428 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 31497 Sorted by residual: bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" C1 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.91e+00 ... (remaining 31492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 41779 1.61 - 3.22: 1008 3.22 - 4.83: 104 4.83 - 6.45: 20 6.45 - 8.06: 1 Bond angle restraints: 42912 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.68 -3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" CA GLY C 219 " pdb=" C GLY C 219 " pdb=" N PHE C 220 " ideal model delta sigma weight residual 114.66 117.95 -3.29 1.10e+00 8.26e-01 8.93e+00 angle pdb=" CA GLY A 667 " pdb=" C GLY A 667 " pdb=" N ALA A 668 " ideal model delta sigma weight residual 114.23 116.59 -2.36 8.80e-01 1.29e+00 7.22e+00 angle pdb=" CA ARG A 237 " pdb=" CB ARG A 237 " pdb=" CG ARG A 237 " ideal model delta sigma weight residual 114.10 119.45 -5.35 2.00e+00 2.50e-01 7.16e+00 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.99e+00 ... (remaining 42907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 17557 17.12 - 34.24: 1377 34.24 - 51.35: 280 51.35 - 68.47: 68 68.47 - 85.59: 26 Dihedral angle restraints: 19308 sinusoidal: 8067 harmonic: 11241 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -151.69 65.69 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 155.76 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 153.91 -60.91 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 19305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4407 0.076 - 0.151: 557 0.151 - 0.227: 10 0.227 - 0.303: 3 0.303 - 0.379: 3 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 4977 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.001 2.00e-02 2.50e+03 1.96e-02 4.79e+00 pdb=" CG ASN C 801 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1315 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.017 2.00e-02 2.50e+03 1.56e-02 4.27e+00 pdb=" CG PHE A 906 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.003 2.00e-02 2.50e+03 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 641 2.68 - 3.23: 29411 3.23 - 3.79: 47537 3.79 - 4.34: 64036 4.34 - 4.90: 107184 Nonbonded interactions: 248809 Sorted by model distance: nonbonded pdb=" O TYR P 114 " pdb=" OH TYR Q 42 " model vdw 2.122 3.040 nonbonded pdb=" O PHE H 71 " pdb=" OG SER H 76 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR C 369 " pdb=" O SER P 110 " model vdw 2.177 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.177 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.196 3.040 ... (remaining 248804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 74.780 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.005 0.064 31590 Z= 0.223 Angle : 0.614 11.469 43149 Z= 0.314 Chirality : 0.046 0.379 4980 Planarity : 0.004 0.053 5475 Dihedral : 12.867 85.591 11976 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 3819 helix: 2.21 (0.20), residues: 613 sheet: -0.35 (0.18), residues: 885 loop : -0.85 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 886 HIS 0.006 0.001 HIS A1064 PHE 0.036 0.002 PHE A 906 TYR 0.024 0.002 TYR B1138 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 2.60420 ( 144) link_BETA1-4 : bond 0.00498 ( 3) link_BETA1-4 : angle 1.84145 ( 9) hydrogen bonds : bond 0.21694 ( 1106) hydrogen bonds : angle 9.10896 ( 3057) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.25333 ( 84) covalent geometry : bond 0.00503 (31497) covalent geometry : angle 0.59392 (42912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 3.387 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.5089 (ppp) cc_final: 0.4861 (ppp) REVERT: A 237 ARG cc_start: 0.7735 (tpt170) cc_final: 0.7192 (tpt170) REVERT: A 950 ASP cc_start: 0.7695 (t0) cc_final: 0.7431 (t0) REVERT: B 1141 LEU cc_start: 0.7942 (mt) cc_final: 0.7703 (tt) REVERT: C 574 ASP cc_start: 0.7503 (t70) cc_final: 0.7137 (t70) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.3577 time to fit residues: 112.5633 Evaluate side-chains 135 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 658 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 0.0270 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 348 optimal weight: 0.3980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 99 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 658 ASN C 239 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 914 ASN C1101 HIS H 6 GLN M 40 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.208562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129936 restraints weight = 49614.378| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.75 r_work: 0.3430 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31590 Z= 0.112 Angle : 0.536 10.380 43149 Z= 0.275 Chirality : 0.045 0.385 4980 Planarity : 0.004 0.047 5475 Dihedral : 6.143 56.568 5225 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.30 % Allowed : 5.00 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3819 helix: 2.32 (0.20), residues: 659 sheet: -0.12 (0.17), residues: 945 loop : -0.86 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.003 0.001 HIS A 207 PHE 0.023 0.001 PHE A 400 TYR 0.027 0.001 TYR A 170 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 48) link_NAG-ASN : angle 2.27949 ( 144) link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 1.22544 ( 9) hydrogen bonds : bond 0.04279 ( 1106) hydrogen bonds : angle 6.63955 ( 3057) SS BOND : bond 0.00221 ( 42) SS BOND : angle 0.92413 ( 84) covalent geometry : bond 0.00235 (31497) covalent geometry : angle 0.51942 (42912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.6053 (m-80) cc_final: 0.5832 (m-80) REVERT: A 66 HIS cc_start: 0.5605 (m90) cc_final: 0.5359 (m90) REVERT: A 238 PHE cc_start: 0.4974 (p90) cc_final: 0.4740 (p90) REVERT: A 950 ASP cc_start: 0.8259 (t0) cc_final: 0.7887 (t0) REVERT: B 914 ASN cc_start: 0.8387 (t0) cc_final: 0.8037 (t0) REVERT: B 1141 LEU cc_start: 0.8083 (mt) cc_final: 0.7648 (tt) REVERT: C 65 PHE cc_start: 0.6959 (m-80) cc_final: 0.6538 (m-10) REVERT: C 612 TYR cc_start: 0.9084 (m-80) cc_final: 0.8801 (m-80) REVERT: H 89 MET cc_start: 0.2282 (mtt) cc_final: 0.1838 (mmp) REVERT: N 105 GLN cc_start: 0.0910 (tm-30) cc_final: 0.0456 (mm-40) outliers start: 10 outliers final: 10 residues processed: 180 average time/residue: 0.3482 time to fit residues: 109.0520 Evaluate side-chains 150 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 237 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 74 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 0.0040 chunk 364 optimal weight: 5.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127704 restraints weight = 49420.649| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.71 r_work: 0.3407 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31590 Z= 0.144 Angle : 0.523 10.170 43149 Z= 0.266 Chirality : 0.045 0.343 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.756 56.671 5223 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.66 % Allowed : 7.65 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3819 helix: 2.29 (0.20), residues: 657 sheet: -0.23 (0.17), residues: 935 loop : -0.88 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS A1064 PHE 0.020 0.001 PHE A 400 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 48) link_NAG-ASN : angle 2.30063 ( 144) link_BETA1-4 : bond 0.00194 ( 3) link_BETA1-4 : angle 1.14939 ( 9) hydrogen bonds : bond 0.03976 ( 1106) hydrogen bonds : angle 6.20568 ( 3057) SS BOND : bond 0.00316 ( 42) SS BOND : angle 0.79354 ( 84) covalent geometry : bond 0.00333 (31497) covalent geometry : angle 0.50568 (42912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5243 (p90) cc_final: 0.4851 (p90) REVERT: A 950 ASP cc_start: 0.8312 (t0) cc_final: 0.7908 (t0) REVERT: A 1144 GLU cc_start: 0.7709 (mp0) cc_final: 0.7491 (mp0) REVERT: B 1141 LEU cc_start: 0.8047 (mt) cc_final: 0.7556 (tt) REVERT: C 65 PHE cc_start: 0.7014 (m-80) cc_final: 0.6427 (m-10) REVERT: C 586 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: C 780 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8094 (mm-30) REVERT: L 37 THR cc_start: 0.4265 (OUTLIER) cc_final: 0.4029 (m) REVERT: M 39 MET cc_start: 0.3934 (tpt) cc_final: 0.0028 (mpp) REVERT: N 105 GLN cc_start: 0.0890 (tm-30) cc_final: 0.0481 (mm-40) outliers start: 22 outliers final: 12 residues processed: 177 average time/residue: 0.3584 time to fit residues: 111.0957 Evaluate side-chains 159 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 31 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 231 optimal weight: 0.2980 chunk 162 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 327 optimal weight: 40.0000 overall best weight: 2.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A1010 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN M 36 ASN M 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.204547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124516 restraints weight = 49517.906| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.73 r_work: 0.3358 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31590 Z= 0.209 Angle : 0.576 10.355 43149 Z= 0.291 Chirality : 0.047 0.342 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.802 59.970 5223 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.26 % Allowed : 9.52 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 3819 helix: 2.09 (0.20), residues: 644 sheet: -0.36 (0.17), residues: 916 loop : -0.95 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 886 HIS 0.007 0.001 HIS A 207 PHE 0.024 0.002 PHE A1121 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 48) link_NAG-ASN : angle 2.47672 ( 144) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 1.25593 ( 9) hydrogen bonds : bond 0.04036 ( 1106) hydrogen bonds : angle 6.09228 ( 3057) SS BOND : bond 0.00457 ( 42) SS BOND : angle 0.88762 ( 84) covalent geometry : bond 0.00492 (31497) covalent geometry : angle 0.55804 (42912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 3.272 Fit side-chains revert: symmetry clash REVERT: A 636 TYR cc_start: 0.4889 (m-10) cc_final: 0.4568 (m-80) REVERT: A 737 ASP cc_start: 0.7865 (t0) cc_final: 0.7499 (t0) REVERT: A 950 ASP cc_start: 0.8328 (t0) cc_final: 0.7902 (t0) REVERT: A 1144 GLU cc_start: 0.7784 (mp0) cc_final: 0.7515 (mp0) REVERT: B 1141 LEU cc_start: 0.8054 (mt) cc_final: 0.7520 (tt) REVERT: C 65 PHE cc_start: 0.7092 (m-80) cc_final: 0.6469 (m-10) REVERT: C 106 PHE cc_start: 0.5881 (m-80) cc_final: 0.5296 (m-80) REVERT: C 869 MET cc_start: 0.9097 (mtm) cc_final: 0.8404 (mtm) REVERT: H 89 MET cc_start: 0.1935 (mtt) cc_final: 0.1580 (mmp) REVERT: M 39 MET cc_start: 0.3992 (tpt) cc_final: 0.0047 (mpp) REVERT: N 105 GLN cc_start: 0.0786 (tm-30) cc_final: 0.0355 (mm-40) REVERT: P 89 MET cc_start: -0.0016 (tmm) cc_final: -0.0428 (ttt) outliers start: 42 outliers final: 29 residues processed: 203 average time/residue: 0.3876 time to fit residues: 138.2226 Evaluate side-chains 177 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 243 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 337 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 283 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 334 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.205358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126145 restraints weight = 49425.156| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.72 r_work: 0.3380 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31590 Z= 0.158 Angle : 0.537 10.503 43149 Z= 0.270 Chirality : 0.045 0.366 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.595 57.439 5223 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.20 % Allowed : 10.75 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3819 helix: 2.18 (0.20), residues: 644 sheet: -0.39 (0.17), residues: 891 loop : -0.94 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 PHE 0.039 0.001 PHE C 92 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 48) link_NAG-ASN : angle 2.39397 ( 144) link_BETA1-4 : bond 0.00251 ( 3) link_BETA1-4 : angle 1.08054 ( 9) hydrogen bonds : bond 0.03696 ( 1106) hydrogen bonds : angle 5.88997 ( 3057) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.40022 ( 84) covalent geometry : bond 0.00367 (31497) covalent geometry : angle 0.51617 (42912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5338 (p90) cc_final: 0.4963 (p90) REVERT: A 636 TYR cc_start: 0.4874 (m-10) cc_final: 0.4603 (m-80) REVERT: A 902 MET cc_start: 0.8756 (tpt) cc_final: 0.8397 (mmt) REVERT: A 950 ASP cc_start: 0.8298 (t0) cc_final: 0.7862 (t0) REVERT: A 1144 GLU cc_start: 0.7866 (mp0) cc_final: 0.7576 (mp0) REVERT: B 200 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 950 ASP cc_start: 0.8556 (m-30) cc_final: 0.8352 (m-30) REVERT: B 1141 LEU cc_start: 0.8042 (mt) cc_final: 0.7485 (tt) REVERT: C 65 PHE cc_start: 0.7045 (m-80) cc_final: 0.6442 (m-10) REVERT: C 869 MET cc_start: 0.9084 (mtm) cc_final: 0.8454 (mtm) REVERT: M 39 MET cc_start: 0.3968 (tpt) cc_final: 0.0089 (mpp) REVERT: N 105 GLN cc_start: 0.0723 (tm-30) cc_final: 0.0346 (mm-40) REVERT: P 89 MET cc_start: 0.0016 (tmm) cc_final: -0.0430 (ttt) outliers start: 40 outliers final: 26 residues processed: 196 average time/residue: 0.3550 time to fit residues: 122.6647 Evaluate side-chains 176 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 253 optimal weight: 0.0030 chunk 241 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 300 optimal weight: 3.9990 chunk 337 optimal weight: 40.0000 chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 804 GLN B 239 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.203608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124144 restraints weight = 49577.753| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.68 r_work: 0.3362 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31590 Z= 0.217 Angle : 0.581 10.242 43149 Z= 0.292 Chirality : 0.047 0.397 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.761 59.454 5223 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.66 % Allowed : 11.62 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3819 helix: 1.99 (0.20), residues: 646 sheet: -0.62 (0.17), residues: 905 loop : -0.98 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.006 0.001 HIS A 207 PHE 0.029 0.002 PHE C 92 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 48) link_NAG-ASN : angle 2.53070 ( 144) link_BETA1-4 : bond 0.00222 ( 3) link_BETA1-4 : angle 1.23100 ( 9) hydrogen bonds : bond 0.03929 ( 1106) hydrogen bonds : angle 5.94294 ( 3057) SS BOND : bond 0.00484 ( 42) SS BOND : angle 1.10786 ( 84) covalent geometry : bond 0.00514 (31497) covalent geometry : angle 0.56125 (42912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 950 ASP cc_start: 0.8402 (t0) cc_final: 0.7953 (t0) REVERT: A 1144 GLU cc_start: 0.7934 (mp0) cc_final: 0.7592 (mp0) REVERT: B 200 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7013 (t80) REVERT: B 1141 LEU cc_start: 0.8131 (mt) cc_final: 0.7575 (tt) REVERT: C 65 PHE cc_start: 0.7121 (m-80) cc_final: 0.6513 (m-10) REVERT: C 569 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7886 (tt) REVERT: C 636 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.5145 (m-10) REVERT: C 869 MET cc_start: 0.9089 (mtm) cc_final: 0.8489 (mtm) REVERT: H 89 MET cc_start: 0.1829 (mtt) cc_final: 0.1539 (mmp) REVERT: M 39 MET cc_start: 0.3974 (tpt) cc_final: -0.0084 (mpp) REVERT: N 105 GLN cc_start: 0.0819 (tm-30) cc_final: 0.0525 (mm-40) REVERT: P 89 MET cc_start: 0.0095 (tmm) cc_final: -0.0375 (ttt) outliers start: 55 outliers final: 42 residues processed: 206 average time/residue: 0.3630 time to fit residues: 132.4705 Evaluate side-chains 196 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 333 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 217 optimal weight: 0.4980 chunk 228 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 376 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN H 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.203434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127948 restraints weight = 49704.258| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.26 r_work: 0.3308 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31590 Z= 0.219 Angle : 0.581 10.298 43149 Z= 0.293 Chirality : 0.047 0.351 4980 Planarity : 0.004 0.065 5475 Dihedral : 5.777 59.741 5223 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.96 % Allowed : 12.50 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3819 helix: 2.04 (0.20), residues: 638 sheet: -0.63 (0.16), residues: 928 loop : -1.02 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 104 HIS 0.005 0.001 HIS A1064 PHE 0.034 0.002 PHE C 92 TYR 0.021 0.001 TYR A1067 ARG 0.010 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 48) link_NAG-ASN : angle 2.54642 ( 144) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 1.17533 ( 9) hydrogen bonds : bond 0.03880 ( 1106) hydrogen bonds : angle 5.91261 ( 3057) SS BOND : bond 0.00490 ( 42) SS BOND : angle 0.98578 ( 84) covalent geometry : bond 0.00519 (31497) covalent geometry : angle 0.56168 (42912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 156 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5146 (ppp) cc_final: 0.4920 (ppp) REVERT: A 238 PHE cc_start: 0.5362 (p90) cc_final: 0.4983 (p90) REVERT: A 402 ILE cc_start: 0.1926 (OUTLIER) cc_final: 0.1669 (mt) REVERT: A 950 ASP cc_start: 0.8388 (t0) cc_final: 0.7944 (t0) REVERT: A 1144 GLU cc_start: 0.7962 (mp0) cc_final: 0.7598 (mp0) REVERT: B 200 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 1141 LEU cc_start: 0.8079 (mt) cc_final: 0.7526 (tt) REVERT: C 65 PHE cc_start: 0.7030 (m-80) cc_final: 0.6430 (m-10) REVERT: C 569 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7795 (tt) REVERT: C 636 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.5189 (m-10) REVERT: C 869 MET cc_start: 0.9063 (mtm) cc_final: 0.8460 (mtm) REVERT: H 89 MET cc_start: 0.1843 (mtt) cc_final: 0.1487 (mmp) REVERT: M 39 MET cc_start: 0.3910 (tpt) cc_final: -0.0083 (mpp) REVERT: N 105 GLN cc_start: 0.0802 (tm-30) cc_final: 0.0543 (mm-40) REVERT: P 89 MET cc_start: 0.0165 (tmm) cc_final: -0.0340 (ttt) outliers start: 65 outliers final: 48 residues processed: 212 average time/residue: 0.3473 time to fit residues: 130.5219 Evaluate side-chains 198 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 139 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 304 optimal weight: 0.6980 chunk 380 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 289 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 285 optimal weight: 0.0970 chunk 256 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.204021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128960 restraints weight = 49610.444| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.11 r_work: 0.3359 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31590 Z= 0.119 Angle : 0.522 10.366 43149 Z= 0.263 Chirality : 0.045 0.339 4980 Planarity : 0.004 0.048 5475 Dihedral : 5.453 56.743 5223 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.63 % Allowed : 12.92 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3819 helix: 2.36 (0.20), residues: 638 sheet: -0.53 (0.16), residues: 928 loop : -0.94 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 104 HIS 0.003 0.001 HIS C 146 PHE 0.035 0.001 PHE C 92 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 48) link_NAG-ASN : angle 2.36491 ( 144) link_BETA1-4 : bond 0.00231 ( 3) link_BETA1-4 : angle 1.00210 ( 9) hydrogen bonds : bond 0.03464 ( 1106) hydrogen bonds : angle 5.64267 ( 3057) SS BOND : bond 0.00272 ( 42) SS BOND : angle 0.81218 ( 84) covalent geometry : bond 0.00268 (31497) covalent geometry : angle 0.50418 (42912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5459 (p90) cc_final: 0.5063 (p90) REVERT: A 402 ILE cc_start: 0.1809 (OUTLIER) cc_final: 0.1536 (mt) REVERT: A 950 ASP cc_start: 0.8366 (t0) cc_final: 0.7907 (t0) REVERT: A 1144 GLU cc_start: 0.7937 (mp0) cc_final: 0.7607 (mp0) REVERT: B 200 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.6903 (t80) REVERT: B 934 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7161 (tp) REVERT: B 1141 LEU cc_start: 0.8075 (mt) cc_final: 0.7507 (tt) REVERT: C 65 PHE cc_start: 0.7161 (m-80) cc_final: 0.6564 (m-10) REVERT: C 569 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7907 (tt) REVERT: C 869 MET cc_start: 0.9047 (mtm) cc_final: 0.8491 (mtm) REVERT: C 1144 GLU cc_start: 0.7833 (mp0) cc_final: 0.7629 (mp0) REVERT: M 39 MET cc_start: 0.3686 (tpt) cc_final: -0.0192 (mpp) REVERT: N 105 GLN cc_start: 0.0850 (tm-30) cc_final: 0.0585 (mm-40) REVERT: P 89 MET cc_start: 0.0198 (OUTLIER) cc_final: -0.0299 (ttt) outliers start: 54 outliers final: 44 residues processed: 196 average time/residue: 0.3577 time to fit residues: 123.7413 Evaluate side-chains 199 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 213 optimal weight: 8.9990 chunk 234 optimal weight: 0.0670 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 223 optimal weight: 5.9990 chunk 336 optimal weight: 40.0000 chunk 134 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.133264 restraints weight = 49442.082| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.52 r_work: 0.3366 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31590 Z= 0.099 Angle : 0.500 10.498 43149 Z= 0.251 Chirality : 0.044 0.353 4980 Planarity : 0.003 0.046 5475 Dihedral : 5.140 55.257 5223 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.51 % Allowed : 13.61 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3819 helix: 2.58 (0.20), residues: 647 sheet: -0.40 (0.17), residues: 919 loop : -0.85 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 104 HIS 0.003 0.000 HIS C1048 PHE 0.022 0.001 PHE C 238 TYR 0.022 0.001 TYR A 170 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 48) link_NAG-ASN : angle 2.25014 ( 144) link_BETA1-4 : bond 0.00406 ( 3) link_BETA1-4 : angle 0.94942 ( 9) hydrogen bonds : bond 0.03257 ( 1106) hydrogen bonds : angle 5.37865 ( 3057) SS BOND : bond 0.00167 ( 42) SS BOND : angle 0.71200 ( 84) covalent geometry : bond 0.00217 (31497) covalent geometry : angle 0.48312 (42912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7542 (t80) cc_final: 0.6959 (t80) REVERT: A 238 PHE cc_start: 0.5256 (p90) cc_final: 0.4889 (p90) REVERT: A 239 GLN cc_start: 0.6521 (tt0) cc_final: 0.6130 (tm-30) REVERT: A 402 ILE cc_start: 0.1786 (OUTLIER) cc_final: 0.1535 (mt) REVERT: A 796 ASP cc_start: 0.8042 (t0) cc_final: 0.7738 (t0) REVERT: A 934 ILE cc_start: 0.8214 (mm) cc_final: 0.7842 (mm) REVERT: A 950 ASP cc_start: 0.8141 (t0) cc_final: 0.7673 (t0) REVERT: A 1144 GLU cc_start: 0.7937 (mp0) cc_final: 0.7615 (mp0) REVERT: B 200 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.6881 (t80) REVERT: C 65 PHE cc_start: 0.7028 (m-80) cc_final: 0.6426 (m-10) REVERT: C 869 MET cc_start: 0.8948 (mtm) cc_final: 0.8400 (mtm) REVERT: C 914 ASN cc_start: 0.8242 (t0) cc_final: 0.8003 (t0) REVERT: H 89 MET cc_start: 0.2550 (mtt) cc_final: 0.2273 (mmt) REVERT: M 39 MET cc_start: 0.3719 (tpt) cc_final: -0.0067 (mpp) REVERT: P 89 MET cc_start: 0.0275 (OUTLIER) cc_final: -0.0199 (ttt) outliers start: 50 outliers final: 41 residues processed: 202 average time/residue: 0.3609 time to fit residues: 128.7144 Evaluate side-chains 196 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 296 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 310 optimal weight: 0.9990 chunk 259 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 317 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 365 optimal weight: 30.0000 chunk 333 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN B 957 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.203475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127732 restraints weight = 49406.003| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.43 r_work: 0.3309 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31590 Z= 0.206 Angle : 0.582 14.087 43149 Z= 0.291 Chirality : 0.047 0.350 4980 Planarity : 0.004 0.046 5475 Dihedral : 5.401 59.882 5223 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.54 % Allowed : 13.61 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 3819 helix: 2.24 (0.20), residues: 638 sheet: -0.51 (0.16), residues: 940 loop : -0.93 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 104 HIS 0.005 0.001 HIS A1064 PHE 0.035 0.002 PHE C 92 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 48) link_NAG-ASN : angle 2.45390 ( 144) link_BETA1-4 : bond 0.00291 ( 3) link_BETA1-4 : angle 1.18318 ( 9) hydrogen bonds : bond 0.03747 ( 1106) hydrogen bonds : angle 5.63207 ( 3057) SS BOND : bond 0.00468 ( 42) SS BOND : angle 0.86044 ( 84) covalent geometry : bond 0.00486 (31497) covalent geometry : angle 0.56416 (42912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 4.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7530 (t80) cc_final: 0.7195 (t80) REVERT: A 239 GLN cc_start: 0.6528 (tt0) cc_final: 0.6243 (tm-30) REVERT: A 796 ASP cc_start: 0.8077 (t0) cc_final: 0.7831 (t0) REVERT: A 950 ASP cc_start: 0.8217 (t0) cc_final: 0.7762 (t0) REVERT: B 200 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7053 (t80) REVERT: C 65 PHE cc_start: 0.7009 (m-80) cc_final: 0.6384 (m-10) REVERT: C 133 PHE cc_start: 0.6710 (m-80) cc_final: 0.6430 (m-80) REVERT: C 569 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7920 (tt) REVERT: H 89 MET cc_start: 0.1983 (mtt) cc_final: 0.1780 (mmt) REVERT: M 39 MET cc_start: 0.3674 (tpt) cc_final: -0.0275 (mpp) REVERT: P 89 MET cc_start: 0.0407 (OUTLIER) cc_final: -0.0173 (ttt) outliers start: 51 outliers final: 42 residues processed: 186 average time/residue: 0.3850 time to fit residues: 128.3552 Evaluate side-chains 188 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 131 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 364 optimal weight: 0.0020 chunk 322 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 overall best weight: 2.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 703 ASN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.203604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129353 restraints weight = 49092.717| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.69 r_work: 0.3301 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31590 Z= 0.186 Angle : 0.573 13.431 43149 Z= 0.286 Chirality : 0.046 0.345 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.449 58.953 5223 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.63 % Allowed : 13.67 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 3819 helix: 2.19 (0.20), residues: 638 sheet: -0.56 (0.16), residues: 928 loop : -0.97 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 104 HIS 0.005 0.001 HIS A 655 PHE 0.023 0.001 PHE A 643 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 48) link_NAG-ASN : angle 2.44540 ( 144) link_BETA1-4 : bond 0.00235 ( 3) link_BETA1-4 : angle 1.13341 ( 9) hydrogen bonds : bond 0.03639 ( 1106) hydrogen bonds : angle 5.63301 ( 3057) SS BOND : bond 0.00408 ( 42) SS BOND : angle 0.81733 ( 84) covalent geometry : bond 0.00440 (31497) covalent geometry : angle 0.55564 (42912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26834.91 seconds wall clock time: 457 minutes 21.17 seconds (27441.17 seconds total)