Starting phenix.real_space_refine on Tue Sep 24 19:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4q_14314/09_2024/7r4q_14314_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4q_14314/09_2024/7r4q_14314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4q_14314/09_2024/7r4q_14314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4q_14314/09_2024/7r4q_14314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4q_14314/09_2024/7r4q_14314_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4q_14314/09_2024/7r4q_14314_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 17309 2.51 5 N 4492 2.21 5 O 5317 1.98 5 H 24182 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 1.90s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51420 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 16380 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1005} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1005} Chain breaks: 8 bond proxies already assigned to first conformer: 16528 Chain: "B" Number of atoms: 16287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 16267 Classifications: {'peptide': 1054} Link IDs: {'PTRANS': 52, 'TRANS': 1001} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1054, 16267 Classifications: {'peptide': 1054} Link IDs: {'PTRANS': 52, 'TRANS': 1001} Chain breaks: 8 bond proxies already assigned to first conformer: 16433 Chain: "C" Number of atoms: 16361 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 9 Conformer: "B" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 9 bond proxies already assigned to first conformer: 16547 Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 895 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 895 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER A 459 " occ=0.60 ... (20 atoms not shown) pdb=" HG BSER A 459 " occ=0.40 residue: pdb=" N ASER B 459 " occ=0.60 ... (20 atoms not shown) pdb=" HG BSER B 459 " occ=0.40 residue: pdb=" N SER D 11 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 11 " occ=0.50 residue: pdb=" N VAL D 12 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D 12 " occ=0.50 residue: pdb=" N SER E 11 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER E 11 " occ=0.50 residue: pdb=" N VAL E 12 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL E 12 " occ=0.50 Time building chain proxies: 33.89, per 1000 atoms: 0.66 Number of scatterers: 51420 At special positions: 0 Unit cell: (148.75, 159.8, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 5317 8.00 N 4492 7.00 C 17309 6.00 H 24182 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " 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 Atom "HETATM51306 O5 NAG B1311 .*. O " rejected from bonding due to valence issues. Atom "HETATM50998 O5 NAG A1303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG B1304 " - " ASN B 282 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 61 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG J 1 " - " ASN C 234 " Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 5.2 seconds 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 22.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.627A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.328A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.619A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.730A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 898 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.056A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.521A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.392A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.107A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.955A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.730A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 898 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.057A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.520A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.618A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.334A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.635A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.730A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 898 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.056A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.521A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.279A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.513A 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: 12.224A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.944A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.319A 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: 5.919A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.825A 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 319 removed outlier: 7.136A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.642A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.168A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.932A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.520A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.280A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.512A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.224A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.944A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.919A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.136A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.651A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.819A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC8, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.933A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.520A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.280A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.512A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.223A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.944A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.919A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.136A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.625A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.933A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.520A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.695A pdb=" N ARG D 38 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.696A pdb=" N ARG E 38 " --> pdb=" O ARG E 47 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3111 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: 21.73 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.39 - 0.68: 13 0.68 - 0.98: 19500 0.98 - 1.27: 9156 1.27 - 1.56: 22993 1.56 - 1.85: 360 Warning: very small bond lengths. Bond restraints: 52022 Sorted by residual: bond pdb=" CB GLN B1106 " pdb=" HB2 GLN B1106 " ideal model delta sigma weight residual 0.970 0.392 0.578 2.00e-02 2.50e+03 8.35e+02 bond pdb=" CB GLN A1106 " pdb=" HB2 GLN A1106 " ideal model delta sigma weight residual 0.970 0.412 0.558 2.00e-02 2.50e+03 7.77e+02 bond pdb=" CB GLN C1106 " pdb=" HB2 GLN C1106 " ideal model delta sigma weight residual 0.970 0.427 0.543 2.00e-02 2.50e+03 7.37e+02 bond pdb=" CE1 PHE C 192 " pdb=" CZ PHE C 192 " ideal model delta sigma weight residual 1.382 0.911 0.471 3.00e-02 1.11e+03 2.47e+02 bond pdb=" CE1 PHE A 192 " pdb=" CZ PHE A 192 " ideal model delta sigma weight residual 1.382 0.912 0.470 3.00e-02 1.11e+03 2.45e+02 ... (remaining 52017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.06: 89848 17.06 - 34.12: 2200 34.12 - 51.18: 498 51.18 - 68.23: 62 68.23 - 85.29: 3 Bond angle restraints: 92611 Sorted by residual: angle pdb=" CA GLN B1106 " pdb=" CB GLN B1106 " pdb=" CG GLN B1106 " ideal model delta sigma weight residual 114.10 179.98 -65.88 2.00e+00 2.50e-01 1.08e+03 angle pdb=" CA GLN A1106 " pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " ideal model delta sigma weight residual 114.10 179.96 -65.86 2.00e+00 2.50e-01 1.08e+03 angle pdb=" CA GLN C1106 " pdb=" CB GLN C1106 " pdb=" CG GLN C1106 " ideal model delta sigma weight residual 114.10 179.93 -65.83 2.00e+00 2.50e-01 1.08e+03 angle pdb=" CD1 TYR A 741 " pdb=" CG TYR A 741 " pdb=" CD2 TYR A 741 " ideal model delta sigma weight residual 118.10 75.09 43.01 1.50e+00 4.44e-01 8.22e+02 angle pdb=" CD1 TYR C 741 " pdb=" CG TYR C 741 " pdb=" CD2 TYR C 741 " ideal model delta sigma weight residual 118.10 75.10 43.00 1.50e+00 4.44e-01 8.22e+02 ... (remaining 92606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 22966 22.93 - 45.86: 2155 45.86 - 68.78: 555 68.78 - 91.71: 62 91.71 - 114.64: 6 Dihedral angle restraints: 25744 sinusoidal: 13968 harmonic: 11776 Sorted by residual: dihedral pdb=" CD1 PHE C 133 " pdb=" CE1 PHE C 133 " pdb=" CZ PHE C 133 " pdb=" HZ PHE C 133 " ideal model delta harmonic sigma weight residual -180.00 -65.36 -114.64 0 5.00e+00 4.00e-02 5.26e+02 dihedral pdb=" CG TYR C 200 " pdb=" CD2 TYR C 200 " pdb=" CE2 TYR C 200 " pdb=" HE2 TYR C 200 " ideal model delta harmonic sigma weight residual 180.00 66.05 113.95 0 5.00e+00 4.00e-02 5.19e+02 dihedral pdb=" CD1 PHE C 43 " pdb=" CE1 PHE C 43 " pdb=" CZ PHE C 43 " pdb=" HZ PHE C 43 " ideal model delta harmonic sigma weight residual -180.00 -77.47 -102.53 0 5.00e+00 4.00e-02 4.20e+02 ... (remaining 25741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.961: 4308 0.961 - 1.922: 30 1.922 - 2.884: 21 2.884 - 3.845: 9 3.845 - 4.806: 15 Chirality restraints: 4383 Sorted by residual: chirality pdb=" CB ILE A 997 " pdb=" CA ILE A 997 " pdb=" CG1 ILE A 997 " pdb=" CG2 ILE A 997 " both_signs ideal model delta sigma weight residual False 2.64 -2.16 4.81 2.00e-01 2.50e+01 5.77e+02 chirality pdb=" CB ILE B 997 " pdb=" CA ILE B 997 " pdb=" CG1 ILE B 997 " pdb=" CG2 ILE B 997 " both_signs ideal model delta sigma weight residual False 2.64 -2.16 4.80 2.00e-01 2.50e+01 5.77e+02 chirality pdb=" CB ILE C 997 " pdb=" CA ILE C 997 " pdb=" CG1 ILE C 997 " pdb=" CG2 ILE C 997 " both_signs ideal model delta sigma weight residual False 2.64 -2.16 4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 4380 not shown) Planarity restraints: 7872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 69 " 0.015 2.00e-02 2.50e+03 2.11e-01 1.00e+03 pdb=" CG HIS C 69 " 0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS C 69 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 HIS C 69 " 0.160 2.00e-02 2.50e+03 pdb=" CE1 HIS C 69 " 0.230 2.00e-02 2.50e+03 pdb=" NE2 HIS C 69 " 0.130 2.00e-02 2.50e+03 pdb=" HD2 HIS C 69 " -0.427 2.00e-02 2.50e+03 pdb=" HE1 HIS C 69 " -0.327 2.00e-02 2.50e+03 pdb=" HE2 HIS C 69 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 655 " -0.085 2.00e-02 2.50e+03 2.04e-01 9.36e+02 pdb=" CG HIS A 655 " 0.262 2.00e-02 2.50e+03 pdb=" ND1 HIS A 655 " -0.395 2.00e-02 2.50e+03 pdb=" CD2 HIS A 655 " 0.142 2.00e-02 2.50e+03 pdb=" CE1 HIS A 655 " -0.212 2.00e-02 2.50e+03 pdb=" NE2 HIS A 655 " 0.058 2.00e-02 2.50e+03 pdb=" HD1 HIS A 655 " 0.226 2.00e-02 2.50e+03 pdb=" HD2 HIS A 655 " -0.106 2.00e-02 2.50e+03 pdb=" HE1 HIS A 655 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 43 " -0.051 2.00e-02 2.50e+03 1.64e-01 8.07e+02 pdb=" CG PHE C 43 " 0.272 2.00e-02 2.50e+03 pdb=" CD1 PHE C 43 " -0.210 2.00e-02 2.50e+03 pdb=" CD2 PHE C 43 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE C 43 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE C 43 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE C 43 " -0.188 2.00e-02 2.50e+03 pdb=" HD1 PHE C 43 " 0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE C 43 " -0.135 2.00e-02 2.50e+03 pdb=" HE1 PHE C 43 " -0.111 2.00e-02 2.50e+03 pdb=" HE2 PHE C 43 " -0.164 2.00e-02 2.50e+03 pdb=" HZ PHE C 43 " 0.295 2.00e-02 2.50e+03 ... (remaining 7869 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.77: 661 1.77 - 2.48: 36218 2.48 - 3.18: 148280 3.18 - 3.89: 199334 3.89 - 4.60: 315252 Nonbonded interactions: 699745 Sorted by model distance: nonbonded pdb=" H LEU C 110 " pdb=" HA LEU C 110 " model vdw 1.059 1.816 nonbonded pdb=" HG2 PRO C 230 " pdb=" HD3 PRO C 230 " model vdw 1.068 1.952 nonbonded pdb=" H GLY B 283 " pdb=" HA2 GLY B 283 " model vdw 1.126 1.816 nonbonded pdb=" H VAL B 70 " pdb=" HA VAL B 70 " model vdw 1.127 1.816 nonbonded pdb=" HE3 LYS C 97 " pdb=" HZ3 LYS C 97 " model vdw 1.184 1.816 ... (remaining 699740 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 1063 or (resid 1064 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 1065 through 1146 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 1063 or (resid 1064 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 1065 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.690 Extract box with map and model: 1.440 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 106.840 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2333 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 : 0.022 0.471 27840 Z= 1.459 Angle : 3.259 65.876 37863 Z= 1.703 Chirality : 0.390 4.806 4383 Planarity : 0.025 0.330 4853 Dihedral : 16.091 106.231 10618 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 30.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.70 % Favored : 91.06 % Rotamer: Outliers : 3.30 % Allowed : 16.49 % Favored : 80.21 % Cbeta Deviations : 3.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 3361 helix: -1.53 (0.18), residues: 704 sheet: -0.97 (0.15), residues: 949 loop : -1.88 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.010 TRP C 886 HIS 0.199 0.049 HIS B 66 PHE 0.304 0.014 PHE A 802 TYR 0.346 0.013 TYR C 741 ARG 0.169 0.010 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 441 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.5796 (tp40) cc_final: 0.4576 (tm-30) REVERT: A 216 LEU cc_start: 0.1337 (OUTLIER) cc_final: -0.1045 (tt) REVERT: A 980 ILE cc_start: 0.3517 (OUTLIER) cc_final: 0.3285 (mp) REVERT: A 1139 ASP cc_start: 0.1852 (t0) cc_final: 0.1556 (t0) REVERT: B 118 LEU cc_start: 0.4735 (pp) cc_final: 0.4171 (pt) REVERT: B 196 ASN cc_start: 0.6591 (t0) cc_final: 0.6030 (p0) REVERT: B 318 PHE cc_start: 0.3639 (OUTLIER) cc_final: 0.2757 (t80) REVERT: B 748 GLU cc_start: 0.2321 (OUTLIER) cc_final: 0.1015 (mp0) REVERT: B 1106 GLN cc_start: -0.0629 (OUTLIER) cc_final: -0.0954 (tt0) REVERT: C 192 PHE cc_start: -0.2955 (OUTLIER) cc_final: -0.4057 (m-80) REVERT: C 900 MET cc_start: 0.1383 (OUTLIER) cc_final: 0.0694 (mmm) REVERT: C 1001 LEU cc_start: 0.5475 (mt) cc_final: 0.5004 (mt) REVERT: D 83 MET cc_start: -0.2037 (mpp) cc_final: -0.2331 (mtt) REVERT: E 59 ASN cc_start: 0.5377 (m110) cc_final: 0.4693 (m-40) outliers start: 96 outliers final: 46 residues processed: 516 average time/residue: 0.7240 time to fit residues: 573.8140 Evaluate side-chains 416 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 363 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 37 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 0.7980 chunk 258 optimal weight: 30.0000 chunk 143 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 309 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 603 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 414 GLN C 616 ASN C 824 ASN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2677 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 27840 Z= 0.381 Angle : 1.329 37.396 37863 Z= 0.648 Chirality : 0.195 3.249 4383 Planarity : 0.010 0.219 4853 Dihedral : 10.473 111.974 4664 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.02 % Allowed : 15.64 % Favored : 79.33 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3361 helix: -0.86 (0.19), residues: 677 sheet: -0.67 (0.16), residues: 903 loop : -1.79 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 111 HIS 0.038 0.007 HIS B 207 PHE 0.057 0.003 PHE A 43 TYR 0.102 0.002 TYR C 741 ARG 0.035 0.002 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 382 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.6109 (p0) REVERT: A 313 TYR cc_start: 0.4245 (m-80) cc_final: 0.3327 (m-80) REVERT: A 546 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5453 (tp) REVERT: A 994 ASP cc_start: 0.1586 (OUTLIER) cc_final: 0.0483 (t70) REVERT: B 196 ASN cc_start: 0.6827 (t0) cc_final: 0.6389 (p0) REVERT: B 318 PHE cc_start: 0.3396 (OUTLIER) cc_final: 0.3096 (t80) REVERT: B 610 VAL cc_start: 0.0779 (OUTLIER) cc_final: -0.0509 (t) REVERT: B 748 GLU cc_start: 0.2030 (pm20) cc_final: 0.1161 (mp0) REVERT: B 991 VAL cc_start: 0.1610 (OUTLIER) cc_final: 0.0929 (t) REVERT: C 99 ASN cc_start: 0.2576 (m110) cc_final: 0.2334 (m110) REVERT: C 726 ILE cc_start: 0.4802 (OUTLIER) cc_final: 0.3978 (pt) REVERT: C 1039 ARG cc_start: 0.5383 (mtp-110) cc_final: 0.4336 (mtp180) REVERT: D 95 TYR cc_start: 0.0598 (OUTLIER) cc_final: -0.1467 (m-80) REVERT: E 59 ASN cc_start: 0.5523 (m110) cc_final: 0.4858 (m-40) outliers start: 147 outliers final: 95 residues processed: 494 average time/residue: 0.7461 time to fit residues: 581.6483 Evaluate side-chains 455 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 352 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 925 ASN Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 108 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 257 optimal weight: 40.0000 chunk 210 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 310 optimal weight: 0.4980 chunk 335 optimal weight: 9.9990 chunk 276 optimal weight: 0.3980 chunk 307 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1005 GLN C1119 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2848 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27840 Z= 0.271 Angle : 1.074 35.516 37863 Z= 0.523 Chirality : 0.171 2.140 4383 Planarity : 0.006 0.097 4853 Dihedral : 9.148 109.559 4620 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.80 % Allowed : 16.62 % Favored : 80.58 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3361 helix: -0.41 (0.19), residues: 678 sheet: -0.54 (0.16), residues: 904 loop : -1.66 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 111 HIS 0.014 0.002 HIS B 207 PHE 0.025 0.002 PHE C1062 TYR 0.033 0.002 TYR C 741 ARG 0.015 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 366 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.1945 (OUTLIER) cc_final: 0.1742 (m90) REVERT: A 121 ASN cc_start: 0.7089 (OUTLIER) cc_final: 0.6291 (p0) REVERT: A 313 TYR cc_start: 0.4363 (m-80) cc_final: 0.3504 (m-80) REVERT: A 825 LYS cc_start: 0.6056 (tptp) cc_final: 0.5522 (tptp) REVERT: B 196 ASN cc_start: 0.6852 (t0) cc_final: 0.6494 (p0) REVERT: B 318 PHE cc_start: 0.3446 (OUTLIER) cc_final: 0.2868 (t80) REVERT: B 610 VAL cc_start: 0.1332 (m) cc_final: -0.0130 (t) REVERT: B 748 GLU cc_start: 0.2099 (pm20) cc_final: 0.1086 (mp0) REVERT: C 54 LEU cc_start: 0.2784 (mt) cc_final: 0.2400 (mp) REVERT: C 1039 ARG cc_start: 0.5386 (mtp-110) cc_final: 0.4920 (mtp180) outliers start: 81 outliers final: 61 residues processed: 429 average time/residue: 0.7454 time to fit residues: 497.5792 Evaluate side-chains 416 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 352 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 208 optimal weight: 0.0570 chunk 311 optimal weight: 0.9980 chunk 329 optimal weight: 20.0000 chunk 162 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 125 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 926 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 321 GLN C 414 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3269 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 27840 Z= 0.285 Angle : 1.009 30.799 37863 Z= 0.499 Chirality : 0.166 2.009 4383 Planarity : 0.006 0.077 4853 Dihedral : 8.270 108.501 4604 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 2.87 % Allowed : 17.46 % Favored : 79.67 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3361 helix: -0.45 (0.19), residues: 685 sheet: -0.48 (0.17), residues: 882 loop : -1.61 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 258 HIS 0.033 0.003 HIS B 49 PHE 0.056 0.002 PHE B 559 TYR 0.032 0.002 TYR A 741 ARG 0.012 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 367 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.2114 (OUTLIER) cc_final: 0.1568 (m-70) REVERT: A 121 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6304 (p0) REVERT: B 196 ASN cc_start: 0.7176 (t0) cc_final: 0.6934 (p0) REVERT: B 610 VAL cc_start: 0.2817 (OUTLIER) cc_final: 0.1552 (t) REVERT: B 741 TYR cc_start: 0.4736 (t80) cc_final: 0.4161 (t80) REVERT: B 767 LEU cc_start: 0.4911 (mt) cc_final: 0.3873 (mt) REVERT: B 1092 GLU cc_start: 0.4739 (OUTLIER) cc_final: 0.3524 (tp30) REVERT: C 54 LEU cc_start: 0.3428 (mt) cc_final: 0.3218 (mp) REVERT: C 1039 ARG cc_start: 0.5566 (mtp-110) cc_final: 0.5241 (mtp-110) REVERT: C 1075 PHE cc_start: 0.0814 (m-80) cc_final: 0.0302 (m-10) outliers start: 83 outliers final: 67 residues processed: 422 average time/residue: 0.7615 time to fit residues: 497.6174 Evaluate side-chains 421 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 350 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 245 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 168 optimal weight: 0.0970 chunk 295 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 613 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3407 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27840 Z= 0.236 Angle : 0.964 32.840 37863 Z= 0.472 Chirality : 0.165 1.880 4383 Planarity : 0.005 0.065 4853 Dihedral : 7.587 107.310 4593 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.46 % Allowed : 18.07 % Favored : 79.47 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3361 helix: -0.05 (0.19), residues: 686 sheet: -0.43 (0.17), residues: 874 loop : -1.60 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 111 HIS 0.011 0.002 HIS A1064 PHE 0.021 0.002 PHE C1062 TYR 0.017 0.001 TYR B 265 ARG 0.009 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 361 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.2050 (OUTLIER) cc_final: 0.1551 (m-70) REVERT: A 129 LYS cc_start: 0.6325 (mtpt) cc_final: 0.6077 (mppt) REVERT: A 825 LYS cc_start: 0.6387 (tptp) cc_final: 0.6015 (tptp) REVERT: B 610 VAL cc_start: 0.3578 (OUTLIER) cc_final: 0.2473 (t) REVERT: B 767 LEU cc_start: 0.5246 (mt) cc_final: 0.4179 (mt) REVERT: B 919 ASN cc_start: 0.5776 (t0) cc_final: 0.5510 (t0) REVERT: B 1092 GLU cc_start: 0.4800 (OUTLIER) cc_final: 0.3610 (tp30) REVERT: C 54 LEU cc_start: 0.3587 (mt) cc_final: 0.3380 (mp) REVERT: C 168 PHE cc_start: 0.6483 (t80) cc_final: 0.6228 (t80) REVERT: C 563 GLN cc_start: 0.5127 (mt0) cc_final: 0.4639 (mt0) REVERT: C 821 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.5214 (mm) REVERT: C 957 GLN cc_start: 0.5846 (tm-30) cc_final: 0.5461 (tm-30) REVERT: C 1039 ARG cc_start: 0.5612 (mtp180) cc_final: 0.5306 (ttm170) outliers start: 71 outliers final: 53 residues processed: 408 average time/residue: 0.7339 time to fit residues: 461.2063 Evaluate side-chains 409 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 352 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 329 optimal weight: 20.0000 chunk 273 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 658 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 658 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 856 ASN C 926 GLN C 965 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4456 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.164 27840 Z= 0.452 Angle : 1.164 31.123 37863 Z= 0.599 Chirality : 0.170 2.022 4383 Planarity : 0.007 0.131 4853 Dihedral : 8.010 107.595 4590 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.99 % Favored : 89.81 % Rotamer: Outliers : 3.30 % Allowed : 17.33 % Favored : 79.37 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.13), residues: 3361 helix: -1.34 (0.18), residues: 674 sheet: -0.90 (0.17), residues: 880 loop : -2.22 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1102 HIS 0.015 0.003 HIS C1048 PHE 0.054 0.003 PHE C1075 TYR 0.037 0.002 TYR B 38 ARG 0.016 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 457 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 LEU cc_start: 0.3204 (OUTLIER) cc_final: 0.2427 (mp) REVERT: B 539 VAL cc_start: 0.5305 (m) cc_final: 0.5096 (m) REVERT: B 950 ASP cc_start: 0.5332 (t0) cc_final: 0.5066 (t0) REVERT: C 534 VAL cc_start: 0.5081 (p) cc_final: 0.4035 (t) REVERT: C 1075 PHE cc_start: 0.2622 (m-80) cc_final: 0.2324 (m-80) REVERT: E 59 ASN cc_start: 0.6204 (OUTLIER) cc_final: 0.5845 (m-40) outliers start: 96 outliers final: 70 residues processed: 505 average time/residue: 0.7487 time to fit residues: 596.6714 Evaluate side-chains 491 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 419 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 111 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 0.0980 chunk 37 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 277 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 205 optimal weight: 0.3980 chunk 200 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 414 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 658 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4337 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27840 Z= 0.238 Angle : 0.974 31.394 37863 Z= 0.485 Chirality : 0.165 1.849 4383 Planarity : 0.006 0.090 4853 Dihedral : 7.260 107.320 4586 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.16 % Allowed : 19.79 % Favored : 78.05 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3361 helix: -0.72 (0.18), residues: 678 sheet: -0.81 (0.17), residues: 868 loop : -2.03 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 111 HIS 0.011 0.002 HIS B1088 PHE 0.030 0.002 PHE B1052 TYR 0.022 0.001 TYR B 707 ARG 0.014 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 432 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 SER cc_start: 0.3283 (OUTLIER) cc_final: 0.3020 (m) REVERT: B 539 VAL cc_start: 0.5127 (m) cc_final: 0.4876 (m) REVERT: B 1092 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4154 (tp30) REVERT: C 534 VAL cc_start: 0.4604 (p) cc_final: 0.3481 (t) REVERT: C 597 VAL cc_start: 0.4442 (OUTLIER) cc_final: 0.4106 (t) REVERT: E 59 ASN cc_start: 0.6000 (m110) cc_final: 0.5692 (m-40) outliers start: 62 outliers final: 46 residues processed: 465 average time/residue: 0.7280 time to fit residues: 525.8209 Evaluate side-chains 463 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 414 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 111 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 258 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4418 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27840 Z= 0.235 Angle : 0.951 31.542 37863 Z= 0.474 Chirality : 0.164 1.815 4383 Planarity : 0.005 0.077 4853 Dihedral : 6.943 105.135 4584 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.79 % Allowed : 19.96 % Favored : 78.25 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 3361 helix: -0.43 (0.19), residues: 683 sheet: -0.69 (0.17), residues: 845 loop : -2.00 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 104 HIS 0.008 0.001 HIS B1088 PHE 0.047 0.002 PHE B 759 TYR 0.031 0.001 TYR B 265 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 422 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 858 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6315 (mt) REVERT: B 297 SER cc_start: 0.3352 (OUTLIER) cc_final: 0.3028 (m) REVERT: B 539 VAL cc_start: 0.5212 (m) cc_final: 0.4953 (m) REVERT: B 1092 GLU cc_start: 0.5230 (OUTLIER) cc_final: 0.4446 (tp30) REVERT: C 534 VAL cc_start: 0.4657 (p) cc_final: 0.3521 (t) REVERT: C 934 ILE cc_start: 0.5475 (mm) cc_final: 0.5086 (mm) REVERT: C 964 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7741 (tppp) REVERT: C 997 ILE cc_start: 0.7131 (pt) cc_final: 0.6659 (mt) REVERT: E 59 ASN cc_start: 0.6047 (m110) cc_final: 0.5761 (m-40) outliers start: 51 outliers final: 40 residues processed: 456 average time/residue: 0.7313 time to fit residues: 522.9173 Evaluate side-chains 458 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 414 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 111 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 1.9990 chunk 314 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 289 optimal weight: 0.0870 chunk 305 optimal weight: 0.3980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 414 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 moved from start: 0.8536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 27840 Z= 0.255 Angle : 0.965 31.495 37863 Z= 0.480 Chirality : 0.166 1.880 4383 Planarity : 0.005 0.063 4853 Dihedral : 6.586 101.978 4580 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.58 % Allowed : 20.60 % Favored : 77.82 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3361 helix: -0.11 (0.19), residues: 685 sheet: -0.67 (0.17), residues: 850 loop : -1.91 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.010 0.002 HIS A1048 PHE 0.025 0.002 PHE B1052 TYR 0.021 0.001 TYR B 756 ARG 0.009 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 458 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.4524 (mmmt) cc_final: 0.2519 (tptp) REVERT: B 294 ASP cc_start: 0.5052 (p0) cc_final: 0.4633 (p0) REVERT: B 351 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6783 (p90) REVERT: B 539 VAL cc_start: 0.5296 (m) cc_final: 0.5016 (m) REVERT: B 870 ILE cc_start: 0.3229 (mt) cc_final: 0.2864 (mt) REVERT: C 534 VAL cc_start: 0.4915 (p) cc_final: 0.3783 (t) REVERT: C 763 LEU cc_start: 0.7074 (mt) cc_final: 0.6714 (mt) REVERT: C 934 ILE cc_start: 0.5776 (mm) cc_final: 0.5344 (mm) REVERT: C 964 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (tptm) REVERT: C 997 ILE cc_start: 0.7161 (pt) cc_final: 0.6770 (mt) REVERT: C 1117 THR cc_start: 0.5877 (p) cc_final: 0.5673 (t) outliers start: 45 outliers final: 35 residues processed: 488 average time/residue: 0.7245 time to fit residues: 549.3598 Evaluate side-chains 492 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 455 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 111 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 1.9990 chunk 323 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 339 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4780 moved from start: 0.9124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27840 Z= 0.269 Angle : 0.967 31.587 37863 Z= 0.482 Chirality : 0.167 1.837 4383 Planarity : 0.005 0.063 4853 Dihedral : 6.450 99.221 4577 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.42 % Allowed : 21.14 % Favored : 77.44 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3361 helix: -0.19 (0.19), residues: 684 sheet: -0.78 (0.17), residues: 871 loop : -1.97 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 104 HIS 0.025 0.002 HIS B1083 PHE 0.030 0.002 PHE B 759 TYR 0.049 0.002 TYR C 204 ARG 0.006 0.001 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 479 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.4796 (mmmt) cc_final: 0.2527 (mmmt) REVERT: A 552 LEU cc_start: 0.5874 (mt) cc_final: 0.5344 (mm) REVERT: A 947 LYS cc_start: 0.5543 (mmmt) cc_final: 0.5302 (mmmt) REVERT: A 1062 PHE cc_start: 0.6447 (m-80) cc_final: 0.5808 (m-80) REVERT: B 38 TYR cc_start: 0.7546 (m-80) cc_final: 0.7280 (m-10) REVERT: B 294 ASP cc_start: 0.5348 (p0) cc_final: 0.5087 (p0) REVERT: B 297 SER cc_start: 0.4856 (OUTLIER) cc_final: 0.4416 (m) REVERT: B 351 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6770 (p90) REVERT: B 539 VAL cc_start: 0.5313 (m) cc_final: 0.5098 (m) REVERT: B 815 ARG cc_start: 0.4813 (ptp-170) cc_final: 0.4573 (ptm160) REVERT: B 1001 LEU cc_start: 0.6719 (mt) cc_final: 0.6389 (mt) REVERT: C 534 VAL cc_start: 0.5391 (p) cc_final: 0.4300 (t) REVERT: C 763 LEU cc_start: 0.7213 (mt) cc_final: 0.6966 (mt) REVERT: C 934 ILE cc_start: 0.5987 (mm) cc_final: 0.5521 (mm) REVERT: C 964 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8065 (tptm) outliers start: 40 outliers final: 32 residues processed: 503 average time/residue: 0.7166 time to fit residues: 563.6580 Evaluate side-chains 508 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 473 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 111 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.199981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.157573 restraints weight = 200637.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.165709 restraints weight = 83953.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.170333 restraints weight = 43149.229| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4385 r_free = 0.4385 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.9197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 27840 Z= 0.314 Angle : 1.042 59.199 37863 Z= 0.546 Chirality : 0.167 1.837 4383 Planarity : 0.005 0.062 4853 Dihedral : 6.413 99.218 4575 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.45 % Allowed : 21.81 % Favored : 76.74 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3361 helix: -0.21 (0.19), residues: 684 sheet: -0.78 (0.17), residues: 871 loop : -1.97 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.025 0.002 HIS B 49 PHE 0.028 0.002 PHE B 759 TYR 0.032 0.002 TYR C 204 ARG 0.017 0.001 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10761.65 seconds wall clock time: 184 minutes 44.30 seconds (11084.30 seconds total)