Starting phenix.real_space_refine on Thu Mar 5 10:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ad1_11719/03_2026/7ad1_11719_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ad1_11719/03_2026/7ad1_11719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ad1_11719/03_2026/7ad1_11719_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ad1_11719/03_2026/7ad1_11719_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ad1_11719/03_2026/7ad1_11719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ad1_11719/03_2026/7ad1_11719.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 13620 2.51 5 N 3550 2.21 5 O 4113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21376 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7129 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 47, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 8, 'PHE:plan': 4, 'GLU:plan': 10, 'TYR:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 217 Chain: "B" Number of atoms: 6724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 6724 Classifications: {'peptide': 935} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 46, 'TRANS': 888} Chain breaks: 13 Unresolved non-hydrogen bonds: 615 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 12, 'ASN:plan1': 19, 'TYR:plan': 14, 'GLN:plan1': 9, 'ARG:plan': 10, 'PHE:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 406 Chain: "C" Number of atoms: 7103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7103 Classifications: {'peptide': 945} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 47, 'TRANS': 897} Chain breaks: 11 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 8, 'ASP:plan': 11, 'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 168 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: F, G, H, I, J, K, L, M, N Time building chain proxies: 5.30, per 1000 atoms: 0.25 Number of scatterers: 21376 At special positions: 0 Unit cell: (160.512, 142.12, 120.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 4113 8.00 N 3550 7.00 C 13620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.02 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 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 813.1 milliseconds 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5318 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 38 sheets defined 28.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.591A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.304A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.922A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.009A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.614A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.620A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.092A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.245A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.044A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.086A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.642A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.969A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.633A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.735A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1034 removed outlier: 4.297A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.143A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.357A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.406A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.215A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.080A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.641A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.921A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.390A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.725A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.298A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.486A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.535A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.024A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.024A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.432A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.113A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.921A 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 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.613A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.784A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.280A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.763A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.829A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.860A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.714A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.688A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.841A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.713A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.469A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.761A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.957A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.626A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2733 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: 5.18 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6374 1.33 - 1.46: 5967 1.46 - 1.59: 9349 1.59 - 1.72: 3 1.72 - 1.85: 114 Bond restraints: 21807 Sorted by residual: bond pdb=" C ASN A 234 " pdb=" N ILE A 235 " ideal model delta sigma weight residual 1.329 1.416 -0.088 1.63e-02 3.76e+03 2.89e+01 bond pdb=" C GLU B1031 " pdb=" N CYS B1032 " ideal model delta sigma weight residual 1.329 1.245 0.084 1.79e-02 3.12e+03 2.21e+01 bond pdb=" C GLU C1031 " pdb=" N CYS C1032 " ideal model delta sigma weight residual 1.329 1.247 0.082 1.79e-02 3.12e+03 2.09e+01 bond pdb=" CG ASN C1098 " pdb=" ND2 ASN C1098 " ideal model delta sigma weight residual 1.328 1.414 -0.086 2.10e-02 2.27e+03 1.69e+01 bond pdb=" CB ASN B1134 " pdb=" CG ASN B1134 " ideal model delta sigma weight residual 1.516 1.423 0.093 2.50e-02 1.60e+03 1.39e+01 ... (remaining 21802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 28063 1.97 - 3.94: 1461 3.94 - 5.91: 186 5.91 - 7.88: 33 7.88 - 9.85: 7 Bond angle restraints: 29750 Sorted by residual: angle pdb=" C ASP C 215 " pdb=" N LEU C 216 " pdb=" CA LEU C 216 " ideal model delta sigma weight residual 120.49 127.13 -6.64 1.42e+00 4.96e-01 2.19e+01 angle pdb=" N THR A 236 " pdb=" CA THR A 236 " pdb=" C THR A 236 " ideal model delta sigma weight residual 110.80 120.65 -9.85 2.13e+00 2.20e-01 2.14e+01 angle pdb=" N ASN C 914 " pdb=" CA ASN C 914 " pdb=" C ASN C 914 " ideal model delta sigma weight residual 111.71 106.51 5.20 1.15e+00 7.56e-01 2.05e+01 angle pdb=" C PHE A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta sigma weight residual 122.36 115.40 6.96 1.60e+00 3.91e-01 1.89e+01 angle pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 108.76 115.77 -7.01 1.69e+00 3.50e-01 1.72e+01 ... (remaining 29745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12190 17.90 - 35.80: 914 35.80 - 53.70: 176 53.70 - 71.61: 40 71.61 - 89.51: 30 Dihedral angle restraints: 13350 sinusoidal: 5141 harmonic: 8209 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 -177.49 -89.51 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.24 84.24 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 133.95 46.05 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 13347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3294 0.105 - 0.210: 304 0.210 - 0.314: 6 0.314 - 0.419: 0 0.419 - 0.524: 1 Chirality restraints: 3605 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 3602 not shown) Planarity restraints: 3824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.020 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR A 453 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " 0.020 2.00e-02 2.50e+03 2.20e-02 8.50e+00 pdb=" CG PHE B 906 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.020 2.00e-02 2.50e+03 1.71e-02 7.28e+00 pdb=" CG TRP C 886 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.007 2.00e-02 2.50e+03 ... (remaining 3821 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 311 2.63 - 3.20: 20128 3.20 - 3.77: 31909 3.77 - 4.33: 44863 4.33 - 4.90: 75769 Nonbonded interactions: 172980 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.066 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.116 3.040 nonbonded pdb=" OH TYR A 170 " pdb=" OG SER A 172 " model vdw 2.126 3.040 nonbonded pdb=" O PRO A1053 " pdb=" NE2 GLN A1054 " model vdw 2.164 3.120 nonbonded pdb=" OG1 THR C 307 " pdb=" OG1 THR C 602 " model vdw 2.185 3.040 ... (remaining 172975 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 65 or resid 82 or (resid 88 and (n \ ame N or name CA or name C or name O or name CB )) or resid 89 through 95 or (re \ sid 96 through 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 through 107 or (resid 108 and (name N or name CA or name C or name O or n \ ame CB )) or resid 109 or (resid 110 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or \ name CA or name C or name O or name CB )) or resid 126 through 168 or (resid 169 \ and (name N or name CA or name C or name O or name CB )) or resid 170 through 1 \ 71 or (resid 172 and (name N or name CA or name C or name O or name CB )) or res \ id 186 through 189 or (resid 190 through 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 196 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 209 or (resid 210 thr \ ough 211 and (name N or name CA or name C or name O or name CB )) or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 21 \ 7 or (resid 218 and (name N or name CA or name C or name O or name CB )) or resi \ d 219 through 223 or (resid 224 and (name N or name CA or name C or name O or na \ me CB )) or resid 225 through 230 or (resid 231 and (name N or name CA or name C \ or name O or name CB )) or resid 232 or (resid 233 and (name N or name CA or na \ me C or name O or name CB )) or resid 234 or (resid 235 through 239 and (name N \ or name CA or name C or name O or name CB )) or resid 240 through 242 or resid 2 \ 65 through 279 or (resid 280 through 281 and (name N or name CA or name C or nam \ e O or name CB )) or resid 282 through 308 or (resid 309 and (name N or name CA \ or name C or name O or name CB )) or resid 310 through 318 or (resid 319 and (na \ me N or name CA or name C or name O or name CB )) or resid 320 through 323 or (r \ esid 324 and (name N or name CA or name C or name O or name CB )) or resid 325 t \ hrough 330 or (resid 331 and (name N or name CA or name C or name O or name CB ) \ ) or resid 332 or (resid 333 through 334 and (name N or name CA or name C or nam \ e O or name CB )) or resid 335 through 346 or (resid 347 through 378 and (name N \ or name CA or name C or name O or name CB )) or resid 379 through 381 or (resid \ 382 through 383 and (name N or name CA or name C or name O or name CB )) or res \ id 384 or (resid 385 through 390 and (name N or name CA or name C or name O or n \ ame CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or name \ C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 413 or (resid 414 through 415 \ and (name N or name CA or name C or name O or name CB )) or resid 416 or (resid \ 417 through 425 and (name N or name CA or name C or name O or name CB )) or resi \ d 426 through 427 or (resid 428 through 430 and (name N or name CA or name C or \ name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (nam \ e N or name CA or name C or name O or name CB )) or resid 463 or (resid 464 thro \ ugh 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or \ (resid 492 through 495 and (name N or name CA or name C or name O or name CB )) \ or (resid 496 through 498 and (name N or name CA or name C or name O or name CB \ )) or resid 499 or (resid 500 through 501 and (name N or name CA or name C or n \ ame O or name CB )) or resid 504 through 509 or (resid 510 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 523 through 525 and (n \ ame N or name CA or name C or name O or name CB )) or resid 526 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 531 or (resid 532 through 534 and (name N or name CA or name C or name O \ or name CB )) or resid 535 through 538 or (resid 539 and (name N or name CA or \ name C or name O or name CB )) or resid 540 through 553 or (resid 554 and (name \ N or name CA or name C or name O or name CB )) or resid 555 through 579 or (resi \ d 580 and (name N or name CA or name C or name O or name CB )) or resid 581 thro \ ugh 675 or resid 690 through 793 or (resid 794 and (name N or name CA or name C \ or name O or name CB )) or resid 795 or (resid 796 and (name N or name CA or nam \ e C or name O or name CB )) or resid 797 through 810 or (resid 811 and (name N o \ r name CA or name C or name O or name CB )) or resid 813 through 824 or (resid 8 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 826 through \ 827 or resid 856 through 866 or (resid 867 through 868 and (name N or name CA o \ r name C or name O or name CB )) or resid 869 through 939 or (resid 940 and (nam \ e N or name CA or name C or name O or name CB )) or resid 941 through 984 or (re \ sid 985 and (name N or name CA or name C or name O or name CB )) or resid 986 th \ rough 987 or (resid 988 through 990 and (name N or name CA or name C or name O o \ r name CB )) or resid 991 through 1085 or (resid 1086 through 1087 and (name N o \ r name CA or name C or name O or name CB )) or resid 1088 through 1100 or (resid \ 1101 and (name N or name CA or name C or name O or name CB )) or resid 1102 thr \ ough 1141 or (resid 1142 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1143 through 1302)) selection = (chain 'B' and (resid 27 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 65 or resi \ d 85 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 96 or (resid 97 and (name N or name CA or name C or name O or nam \ e CB )) or resid 98 or (resid 99 and (name N or name CA or name C or name O or n \ ame CB )) or resid 100 through 104 or (resid 105 through 106 and (name N or name \ CA or name C or name O or name CB )) or resid 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 or (resid 110 through 113 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 1 \ 20 or (resid 121 and (name N or name CA or name C or name O or name CB )) or res \ id 122 through 128 or (resid 129 and (name N or name CA or name C or name O or n \ ame CB )) or resid 130 through 131 or resid 166 through 168 or (resid 169 and (n \ ame N or name CA or name C or name O or name CB )) or resid 170 through 189 or ( \ resid 190 through 191 and (name N or name CA or name C or name O or name CB )) o \ r resid 192 through 195 or (resid 196 through 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or (resid 210 through 215 an \ d (name N or name CA or name C or name O or name CB )) or resid 216 through 219 \ or (resid 220 and (name N or name CA or name C or name O or name CB )) or resid \ 221 through 230 or (resid 231 and (name N or name CA or name C or name O or name \ CB )) or resid 232 or (resid 233 and (name N or name CA or name C or name O or \ name CB )) or resid 234 or (resid 235 through 239 and (name N or name CA or name \ C or name O or name CB )) or resid 240 through 241 or (resid 242 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 269 or (resid 27 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 271 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 323 or (resid 324 and (name N or name CA or name C or name O or \ name CB )) or resid 325 through 327 or (resid 328 and (name N or name CA or name \ C or name O or name CB )) or resid 329 through 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 360 or (resid 36 \ 1 through 378 and (name N or name CA or name C or name O or name CB )) or resid \ 379 through 442 or resid 463 through 502 or resid 505 through 524 or (resid 525 \ and (name N or name CA or name C or name O or name CB )) or resid 526 through 53 \ 6 or (resid 537 and (name N or name CA or name C or name O or name CB )) or resi \ d 538 through 567 or (resid 568 and (name N or name CA or name C or name O or na \ me CB )) or resid 569 through 581 or (resid 582 through 583 and (name N or name \ CA or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and \ (name N or name CA or name C or name O or name CB )) or resid 587 through 595 or \ (resid 596 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 7 through 618 or (resid 619 and (name N or name CA or name C or name O or name C \ B )) or resid 620 through 675 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 786 or (resid \ 787 and (name N or name CA or name C or name O or name CB )) or resid 788 throu \ gh 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or \ resid 813 through 824 or (resid 825 and (name N or name CA or name C or name O \ or name CB )) or resid 826 through 827 or resid 856 through 866 or (resid 867 th \ rough 868 and (name N or name CA or name C or name O or name CB )) or resid 869 \ through 920 or (resid 921 and (name N or name CA or name C or name O or name CB \ )) or resid 922 through 939 or (resid 940 and (name N or name CA or name C or na \ me O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA \ or name C or name O or name CB )) or resid 986 through 987 or (resid 988 throug \ h 990 and (name N or name CA or name C or name O or name CB )) or resid 991 thro \ ugh 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) \ or resid 1074 through 1100 or (resid 1101 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1102 through 1117 or (resid 1118 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1119 through 1134 or (resid 1135 \ and (name N or name CA or name C or name O or name CB )) or resid 1136 through \ 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1147 through 1302)) selection = (chain 'C' and (resid 27 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 52 or (resid 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 65 or resi \ d 85 or resid 88 through 95 or (resid 96 through 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 or (resid 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 104 or (resid 105 through 10 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 107 through \ 110 or (resid 111 through 113 and (name N or name CA or name C or name O or name \ CB )) or resid 116 through 120 or (resid 121 and (name N or name CA or name C o \ r name O or name CB )) or resid 122 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 195 or (resid 196 an \ d (name N or name CA or name C or name O or name CB )) or (resid 200 and (name N \ or name CA or name C or name O or name CB )) or resid 201 through 211 or resid \ 215 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 or (resid 220 and (name N or name CA or name C or name O or \ name CB )) or resid 221 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 238 or (resid 239 and (name N or \ name CA or name C or name O or name CB )) or resid 240 through 242 or resid 265 \ through 269 or (resid 270 and (name N or name CA or name C or name O or name CB \ )) or resid 271 through 279 or (resid 280 through 281 and (name N or name CA or \ name C or name O or name CB )) or resid 282 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 318 or (res \ id 319 and (name N or name CA or name C or name O or name CB )) or resid 320 thr \ ough 327 or (resid 328 and (name N or name CA or name C or name O or name CB )) \ or resid 329 through 330 or (resid 331 and (name N or name CA or name C or name \ O or name CB )) or resid 332 or (resid 333 through 334 and (name N or name CA or \ name C or name O or name CB )) or resid 335 or (resid 336 and (name N or name C \ A or name C or name O or name CB )) or resid 337 through 344 or (resid 345 throu \ gh 378 and (name N or name CA or name C or name O or name CB )) or resid 379 or \ (resid 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 383 and (name N or name CA or name C or name O or name CB \ )) or resid 384 or (resid 385 through 390 and (name N or name CA or name C or n \ ame O or name CB )) or resid 391 or (resid 392 through 403 and (name N or name C \ A or name C or name O or name CB )) or (resid 404 through 411 and (name N or nam \ e CA or name C or name O or name CB )) or resid 412 through 413 or (resid 414 th \ rough 415 and (name N or name CA or name C or name O or name CB )) or (resid 416 \ through 425 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 26 or (resid 427 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 through 433 or (resid 434 through 442 and (name N or name CA \ or name C or name O or name CB )) or resid 463 or (resid 464 through 466 and (na \ me N or name CA or name C or name O or name CB )) or resid 491 or (resid 492 thr \ ough 495 and (name N or name CA or name C or name O or name CB )) or resid 496 o \ r (resid 497 through 498 and (name N or name CA or name C or name O or name CB ) \ ) or resid 499 through 500 or (resid 501 and (name N or name CA or name C or nam \ e O or name CB )) or resid 502 or (resid 505 through 506 and (name N or name CA \ or name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (na \ me N or name CA or name C or name O or name CB )) or (resid 523 through 525 and \ (name N or name CA or name C or name O or name CB )) or resid 526 through 527 or \ (resid 528 through 529 and (name N or name CA or name C or name O or name CB )) \ or resid 530 through 531 or (resid 532 through 534 and (name N or name CA or na \ me C or name O or name CB )) or resid 535 through 536 or (resid 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 or (resid 539 and (nam \ e N or name CA or name C or name O or name CB )) or resid 540 through 553 or (re \ sid 554 and (name N or name CA or name C or name O or name CB )) or resid 555 th \ rough 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) \ or resid 569 through 570 or (resid 571 and (name N or name CA or name C or name \ O or name CB )) or resid 572 through 579 or (resid 580 and (name N or name CA o \ r name C or name O or name CB )) or resid 581 or (resid 582 through 583 and (nam \ e N or name CA or name C or name O or name CB )) or resid 584 through 585 or (re \ sid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 th \ rough 595 or (resid 596 and (name N or name CA or name C or name O or name CB )) \ or resid 597 through 618 or (resid 619 and (name N or name CA or name C or name \ O or name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N \ or name CA or name C or name O or name CB )) or resid 648 through 675 or resid 6 \ 90 through 786 or (resid 787 and (name N or name CA or name C or name O or name \ CB )) or resid 788 through 793 or (resid 794 and (name N or name CA or name C or \ name O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name \ C or name O or name CB )) or resid 797 through 920 or (resid 921 and (name N or \ name CA or name C or name O or name CB )) or resid 922 through 989 or (resid 990 \ and (name N or name CA or name C or name O or name CB )) or resid 991 through 1 \ 072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or r \ esid 1074 through 1085 or (resid 1086 through 1087 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1088 through 1117 or (resid 1118 and (name \ N or name CA or name C or name O or name CB )) or resid 1119 through 1141 or (re \ sid 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 \ or (resid 1144 through 1146 and (name N or name CA or name C or name O or name C \ B )) or resid 1147 through 1302)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.040 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.016 0.141 21871 Z= 0.693 Angle : 1.050 21.837 29908 Z= 0.553 Chirality : 0.062 0.524 3605 Planarity : 0.006 0.067 3804 Dihedral : 13.733 87.668 7930 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.15), residues: 2750 helix: -0.10 (0.19), residues: 692 sheet: -1.25 (0.17), residues: 647 loop : -2.15 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1019 TYR 0.071 0.003 TYR A 453 PHE 0.050 0.003 PHE B 906 TRP 0.041 0.004 TRP C 886 HIS 0.009 0.003 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.01577 (21807) covalent geometry : angle 0.98870 (29750) SS BOND : bond 0.00842 ( 34) SS BOND : angle 2.31466 ( 68) hydrogen bonds : bond 0.13340 ( 1007) hydrogen bonds : angle 8.18023 ( 2733) link_BETA1-4 : bond 0.00197 ( 10) link_BETA1-4 : angle 2.24860 ( 30) link_NAG-ASN : bond 0.02768 ( 20) link_NAG-ASN : angle 7.46779 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.802 Fit side-chains REVERT: A 409 GLN cc_start: 0.6498 (mp10) cc_final: 0.6271 (mp10) REVERT: A 740 MET cc_start: 0.8020 (tpt) cc_final: 0.7671 (tpt) REVERT: B 318 PHE cc_start: 0.6884 (t80) cc_final: 0.6545 (t80) REVERT: B 567 ARG cc_start: 0.7614 (mmt90) cc_final: 0.7158 (mmt90) REVERT: B 740 MET cc_start: 0.7950 (ttm) cc_final: 0.7747 (ttt) REVERT: B 964 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7621 (mppt) REVERT: B 1136 THR cc_start: 0.8781 (m) cc_final: 0.8408 (p) REVERT: C 342 PHE cc_start: 0.7600 (m-80) cc_final: 0.7278 (m-80) REVERT: C 408 ARG cc_start: 0.6996 (ppt170) cc_final: 0.6441 (ttp-110) REVERT: C 529 LYS cc_start: 0.8572 (mmpt) cc_final: 0.8307 (mmmm) REVERT: C 646 ARG cc_start: 0.7473 (ttt180) cc_final: 0.7261 (ttm110) REVERT: C 776 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8149 (ttpt) REVERT: C 935 GLN cc_start: 0.7941 (mt0) cc_final: 0.7551 (mt0) REVERT: C 1002 GLN cc_start: 0.7527 (tt0) cc_final: 0.7312 (tt0) outliers start: 0 outliers final: 1 residues processed: 173 average time/residue: 0.6207 time to fit residues: 122.5557 Evaluate side-chains 107 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 436 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 613 GLN B 658 ASN B 955 ASN B1101 HIS C 675 GLN C 872 GLN C1071 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099077 restraints weight = 34063.173| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.09 r_work: 0.3176 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21871 Z= 0.143 Angle : 0.623 14.317 29908 Z= 0.319 Chirality : 0.045 0.241 3605 Planarity : 0.004 0.049 3804 Dihedral : 6.791 59.856 3593 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.06 % Allowed : 5.30 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2750 helix: 1.53 (0.20), residues: 685 sheet: -0.88 (0.18), residues: 612 loop : -1.59 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 237 TYR 0.019 0.001 TYR C1067 PHE 0.015 0.001 PHE A 400 TRP 0.012 0.001 TRP C 64 HIS 0.002 0.000 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00314 (21807) covalent geometry : angle 0.60114 (29750) SS BOND : bond 0.00358 ( 34) SS BOND : angle 0.95670 ( 68) hydrogen bonds : bond 0.04805 ( 1007) hydrogen bonds : angle 6.37041 ( 2733) link_BETA1-4 : bond 0.00527 ( 10) link_BETA1-4 : angle 1.67192 ( 30) link_NAG-ASN : bond 0.00798 ( 20) link_NAG-ASN : angle 3.42975 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6641 (t60) cc_final: 0.6331 (t60) REVERT: A 335 LEU cc_start: 0.7458 (mm) cc_final: 0.7065 (mt) REVERT: A 436 TRP cc_start: 0.6482 (p90) cc_final: 0.6254 (p90) REVERT: A 697 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8923 (ptt) REVERT: A 740 MET cc_start: 0.8976 (tpt) cc_final: 0.8742 (tpt) REVERT: A 994 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: A 1072 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: B 237 ARG cc_start: 0.6607 (mtp-110) cc_final: 0.6190 (mtp85) REVERT: B 564 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6762 (mt0) REVERT: B 567 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7811 (mmt90) REVERT: B 577 ARG cc_start: 0.6397 (ttm-80) cc_final: 0.6060 (ttm-80) REVERT: B 957 GLN cc_start: 0.8581 (tt0) cc_final: 0.8312 (tp-100) REVERT: C 342 PHE cc_start: 0.7634 (m-80) cc_final: 0.7386 (m-80) REVERT: C 957 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7798 (tp40) outliers start: 23 outliers final: 8 residues processed: 159 average time/residue: 0.5680 time to fit residues: 104.1405 Evaluate side-chains 125 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 193 optimal weight: 0.5980 chunk 217 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 334 ASN A 409 GLN A1119 ASN B1010 GLN B1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099258 restraints weight = 33974.708| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.13 r_work: 0.3142 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21871 Z= 0.195 Angle : 0.621 12.385 29908 Z= 0.316 Chirality : 0.046 0.196 3605 Planarity : 0.004 0.046 3804 Dihedral : 6.145 49.267 3593 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.89 % Allowed : 8.44 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2750 helix: 1.90 (0.21), residues: 684 sheet: -0.56 (0.19), residues: 603 loop : -1.42 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.022 0.002 TYR A1067 PHE 0.030 0.002 PHE B 541 TRP 0.017 0.002 TRP C 886 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00452 (21807) covalent geometry : angle 0.60039 (29750) SS BOND : bond 0.00417 ( 34) SS BOND : angle 1.00259 ( 68) hydrogen bonds : bond 0.04988 ( 1007) hydrogen bonds : angle 6.14688 ( 2733) link_BETA1-4 : bond 0.00326 ( 10) link_BETA1-4 : angle 1.73320 ( 30) link_NAG-ASN : bond 0.00606 ( 20) link_NAG-ASN : angle 3.25502 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6427 (ptp-170) cc_final: 0.6223 (ptt180) REVERT: A 335 LEU cc_start: 0.7528 (mm) cc_final: 0.7049 (mt) REVERT: A 697 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8982 (ptt) REVERT: A 740 MET cc_start: 0.8996 (tpt) cc_final: 0.8764 (tpt) REVERT: A 994 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: B 564 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6825 (mt0) REVERT: B 577 ARG cc_start: 0.6411 (ttm-80) cc_final: 0.6019 (ttm-80) REVERT: B 607 GLN cc_start: 0.8323 (tt0) cc_final: 0.7907 (mm-40) REVERT: B 619 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: B 964 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8285 (mppt) REVERT: C 342 PHE cc_start: 0.7617 (m-80) cc_final: 0.7397 (m-80) REVERT: C 408 ARG cc_start: 0.7024 (pmt-80) cc_final: 0.6794 (pmt-80) REVERT: C 957 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7776 (tp40) outliers start: 41 outliers final: 17 residues processed: 147 average time/residue: 0.5519 time to fit residues: 94.9587 Evaluate side-chains 135 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 207 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 193 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1135 ASN C 787 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.139913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098152 restraints weight = 33918.400| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.14 r_work: 0.3143 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21871 Z= 0.182 Angle : 0.591 11.810 29908 Z= 0.302 Chirality : 0.046 0.184 3605 Planarity : 0.004 0.049 3804 Dihedral : 5.847 59.463 3593 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.66 % Allowed : 9.87 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2750 helix: 1.98 (0.21), residues: 684 sheet: -0.46 (0.19), residues: 589 loop : -1.32 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.019 0.002 TYR B1067 PHE 0.030 0.001 PHE B 541 TRP 0.013 0.002 TRP C 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00426 (21807) covalent geometry : angle 0.57275 (29750) SS BOND : bond 0.00381 ( 34) SS BOND : angle 0.96790 ( 68) hydrogen bonds : bond 0.04742 ( 1007) hydrogen bonds : angle 6.02862 ( 2733) link_BETA1-4 : bond 0.00257 ( 10) link_BETA1-4 : angle 1.41232 ( 30) link_NAG-ASN : bond 0.00509 ( 20) link_NAG-ASN : angle 3.02884 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4658 (m-40) cc_final: 0.3970 (p0) REVERT: A 64 TRP cc_start: 0.6711 (t60) cc_final: 0.6365 (t60) REVERT: A 697 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.9017 (ptt) REVERT: A 740 MET cc_start: 0.9011 (tpt) cc_final: 0.8764 (tpt) REVERT: A 994 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: B 130 VAL cc_start: 0.7892 (t) cc_final: 0.7658 (p) REVERT: B 564 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6757 (mt0) REVERT: B 577 ARG cc_start: 0.6364 (ttm-80) cc_final: 0.5999 (ttm-80) REVERT: B 586 ASP cc_start: 0.7169 (m-30) cc_final: 0.6805 (m-30) REVERT: B 607 GLN cc_start: 0.8324 (tt0) cc_final: 0.7903 (mm-40) REVERT: B 619 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: B 964 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8212 (mppt) REVERT: B 1135 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7982 (m110) REVERT: C 342 PHE cc_start: 0.7691 (m-80) cc_final: 0.7444 (m-80) REVERT: C 408 ARG cc_start: 0.6923 (pmt-80) cc_final: 0.6633 (pmt-80) REVERT: C 957 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7783 (tp40) outliers start: 36 outliers final: 20 residues processed: 148 average time/residue: 0.5399 time to fit residues: 93.1587 Evaluate side-chains 140 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 276 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 117 optimal weight: 0.0000 chunk 54 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100679 restraints weight = 33578.198| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.14 r_work: 0.3173 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21871 Z= 0.130 Angle : 0.554 10.979 29908 Z= 0.283 Chirality : 0.044 0.169 3605 Planarity : 0.004 0.047 3804 Dihedral : 5.520 55.605 3593 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.52 % Allowed : 11.16 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2750 helix: 2.15 (0.21), residues: 684 sheet: -0.36 (0.19), residues: 602 loop : -1.25 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 646 TYR 0.020 0.001 TYR A 423 PHE 0.032 0.001 PHE B 541 TRP 0.012 0.001 TRP C 64 HIS 0.002 0.000 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00293 (21807) covalent geometry : angle 0.53466 (29750) SS BOND : bond 0.00322 ( 34) SS BOND : angle 1.34284 ( 68) hydrogen bonds : bond 0.04316 ( 1007) hydrogen bonds : angle 5.85175 ( 2733) link_BETA1-4 : bond 0.00340 ( 10) link_BETA1-4 : angle 1.33056 ( 30) link_NAG-ASN : bond 0.00412 ( 20) link_NAG-ASN : angle 2.83805 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.746 Fit side-chains REVERT: A 61 ASN cc_start: 0.4693 (m-40) cc_final: 0.3971 (p0) REVERT: A 64 TRP cc_start: 0.6577 (t60) cc_final: 0.6297 (t60) REVERT: A 400 PHE cc_start: 0.7865 (p90) cc_final: 0.7614 (p90) REVERT: A 697 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9009 (ptt) REVERT: A 740 MET cc_start: 0.8965 (tpt) cc_final: 0.8711 (tpt) REVERT: A 994 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: B 564 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6705 (mt0) REVERT: B 577 ARG cc_start: 0.6272 (ttm-80) cc_final: 0.5931 (ttm-80) REVERT: B 586 ASP cc_start: 0.7078 (m-30) cc_final: 0.6766 (m-30) REVERT: B 607 GLN cc_start: 0.8239 (tt0) cc_final: 0.7836 (mm-40) REVERT: B 964 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8173 (mppt) REVERT: C 342 PHE cc_start: 0.7726 (m-80) cc_final: 0.7484 (m-80) REVERT: C 408 ARG cc_start: 0.6928 (pmt-80) cc_final: 0.6598 (pmt-80) REVERT: C 957 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7754 (tp40) outliers start: 33 outliers final: 19 residues processed: 148 average time/residue: 0.5317 time to fit residues: 92.0215 Evaluate side-chains 138 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 254 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.140220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099112 restraints weight = 33601.959| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.12 r_work: 0.3153 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21871 Z= 0.167 Angle : 0.575 9.937 29908 Z= 0.294 Chirality : 0.045 0.175 3605 Planarity : 0.004 0.051 3804 Dihedral : 5.412 49.520 3593 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.98 % Allowed : 11.58 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2750 helix: 2.17 (0.21), residues: 676 sheet: -0.34 (0.19), residues: 603 loop : -1.20 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 646 TYR 0.019 0.001 TYR B1067 PHE 0.033 0.001 PHE B 541 TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00390 (21807) covalent geometry : angle 0.55676 (29750) SS BOND : bond 0.00344 ( 34) SS BOND : angle 1.34787 ( 68) hydrogen bonds : bond 0.04580 ( 1007) hydrogen bonds : angle 5.85912 ( 2733) link_BETA1-4 : bond 0.00313 ( 10) link_BETA1-4 : angle 1.38379 ( 30) link_NAG-ASN : bond 0.00489 ( 20) link_NAG-ASN : angle 2.86504 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4536 (m-40) cc_final: 0.3918 (p0) REVERT: A 400 PHE cc_start: 0.7956 (p90) cc_final: 0.7667 (p90) REVERT: A 697 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9039 (ptt) REVERT: A 740 MET cc_start: 0.8998 (tpt) cc_final: 0.8725 (tpt) REVERT: A 994 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: B 564 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6717 (mt0) REVERT: B 577 ARG cc_start: 0.6380 (ttm-80) cc_final: 0.6054 (ttm-80) REVERT: B 586 ASP cc_start: 0.7027 (m-30) cc_final: 0.6715 (m-30) REVERT: B 607 GLN cc_start: 0.8219 (tt0) cc_final: 0.7825 (mm-40) REVERT: B 619 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: B 964 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8230 (mppt) REVERT: C 342 PHE cc_start: 0.7737 (m-80) cc_final: 0.7530 (m-80) REVERT: C 957 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7784 (tp40) outliers start: 43 outliers final: 27 residues processed: 149 average time/residue: 0.5168 time to fit residues: 91.3232 Evaluate side-chains 148 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 167 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 chunk 96 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 114 optimal weight: 0.1980 chunk 181 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B1135 ASN C 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.141610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104150 restraints weight = 33735.756| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.18 r_work: 0.3185 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21871 Z= 0.110 Angle : 0.522 9.719 29908 Z= 0.269 Chirality : 0.043 0.162 3605 Planarity : 0.004 0.053 3804 Dihedral : 5.032 49.922 3593 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.71 % Allowed : 12.22 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2750 helix: 2.37 (0.21), residues: 673 sheet: -0.38 (0.19), residues: 631 loop : -1.08 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 646 TYR 0.016 0.001 TYR B1067 PHE 0.034 0.001 PHE B 541 TRP 0.011 0.001 TRP C 64 HIS 0.001 0.000 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00243 (21807) covalent geometry : angle 0.50680 (29750) SS BOND : bond 0.00263 ( 34) SS BOND : angle 1.04263 ( 68) hydrogen bonds : bond 0.04055 ( 1007) hydrogen bonds : angle 5.66954 ( 2733) link_BETA1-4 : bond 0.00354 ( 10) link_BETA1-4 : angle 1.20746 ( 30) link_NAG-ASN : bond 0.00382 ( 20) link_NAG-ASN : angle 2.59498 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4526 (m-40) cc_final: 0.4033 (p0) REVERT: A 64 TRP cc_start: 0.6548 (t60) cc_final: 0.6311 (t60) REVERT: A 400 PHE cc_start: 0.7927 (p90) cc_final: 0.7725 (p90) REVERT: A 697 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.9035 (ptt) REVERT: A 740 MET cc_start: 0.9002 (tpt) cc_final: 0.8743 (tpt) REVERT: A 994 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: B 607 GLN cc_start: 0.8222 (tt0) cc_final: 0.7886 (mm-40) REVERT: B 619 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: B 957 GLN cc_start: 0.8600 (tt0) cc_final: 0.8341 (tp-100) REVERT: B 964 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8194 (mppt) REVERT: C 957 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7810 (tp40) outliers start: 37 outliers final: 25 residues processed: 148 average time/residue: 0.5023 time to fit residues: 87.8705 Evaluate side-chains 141 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 279 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 191 optimal weight: 0.3980 chunk 256 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103650 restraints weight = 33718.132| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.20 r_work: 0.3175 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21871 Z= 0.130 Angle : 0.537 9.270 29908 Z= 0.275 Chirality : 0.044 0.178 3605 Planarity : 0.004 0.053 3804 Dihedral : 4.969 53.920 3593 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.08 % Allowed : 12.41 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2750 helix: 2.37 (0.21), residues: 679 sheet: -0.31 (0.19), residues: 633 loop : -1.01 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 646 TYR 0.018 0.001 TYR B1067 PHE 0.033 0.001 PHE B 541 TRP 0.012 0.001 TRP C 64 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (21807) covalent geometry : angle 0.52232 (29750) SS BOND : bond 0.00282 ( 34) SS BOND : angle 1.03196 ( 68) hydrogen bonds : bond 0.04186 ( 1007) hydrogen bonds : angle 5.65953 ( 2733) link_BETA1-4 : bond 0.00347 ( 10) link_BETA1-4 : angle 1.25013 ( 30) link_NAG-ASN : bond 0.00388 ( 20) link_NAG-ASN : angle 2.58447 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4525 (m-40) cc_final: 0.4064 (p0) REVERT: A 64 TRP cc_start: 0.6520 (t60) cc_final: 0.6267 (t60) REVERT: A 378 LYS cc_start: 0.7535 (tttt) cc_final: 0.6931 (tmtp) REVERT: A 400 PHE cc_start: 0.7941 (p90) cc_final: 0.7727 (p90) REVERT: A 697 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9034 (ptt) REVERT: A 994 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: B 564 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6662 (mt0) REVERT: B 577 ARG cc_start: 0.6391 (ttm-80) cc_final: 0.6036 (ttm-80) REVERT: B 607 GLN cc_start: 0.8260 (tt0) cc_final: 0.7897 (mm-40) REVERT: B 619 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 957 GLN cc_start: 0.8602 (tt0) cc_final: 0.8341 (tp-100) REVERT: B 964 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8216 (mppt) REVERT: C 957 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7819 (tp40) outliers start: 45 outliers final: 31 residues processed: 153 average time/residue: 0.5008 time to fit residues: 90.9485 Evaluate side-chains 153 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 114 optimal weight: 0.0980 chunk 175 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100095 restraints weight = 33784.295| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.11 r_work: 0.3183 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21871 Z= 0.121 Angle : 0.524 8.929 29908 Z= 0.269 Chirality : 0.043 0.161 3605 Planarity : 0.004 0.054 3804 Dihedral : 4.919 59.226 3593 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.80 % Allowed : 12.82 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2750 helix: 2.39 (0.21), residues: 680 sheet: -0.29 (0.19), residues: 659 loop : -0.99 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 646 TYR 0.020 0.001 TYR A 423 PHE 0.034 0.001 PHE B 541 TRP 0.012 0.001 TRP C 64 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00276 (21807) covalent geometry : angle 0.50966 (29750) SS BOND : bond 0.00265 ( 34) SS BOND : angle 0.95547 ( 68) hydrogen bonds : bond 0.04063 ( 1007) hydrogen bonds : angle 5.56708 ( 2733) link_BETA1-4 : bond 0.00360 ( 10) link_BETA1-4 : angle 1.18847 ( 30) link_NAG-ASN : bond 0.00353 ( 20) link_NAG-ASN : angle 2.48015 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4318 (m-40) cc_final: 0.4025 (p0) REVERT: A 64 TRP cc_start: 0.6518 (t60) cc_final: 0.6226 (t60) REVERT: A 241 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5139 (pp) REVERT: A 319 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7773 (mtp85) REVERT: A 378 LYS cc_start: 0.7523 (tttt) cc_final: 0.6903 (tmtp) REVERT: A 400 PHE cc_start: 0.7864 (p90) cc_final: 0.7658 (p90) REVERT: A 697 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.9020 (ptt) REVERT: A 994 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: B 203 ILE cc_start: 0.8139 (tt) cc_final: 0.7807 (pt) REVERT: B 607 GLN cc_start: 0.8257 (tt0) cc_final: 0.7882 (mm-40) REVERT: B 619 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: B 957 GLN cc_start: 0.8603 (tt0) cc_final: 0.8337 (tp-100) REVERT: B 964 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8184 (mppt) REVERT: C 957 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7819 (tp40) outliers start: 39 outliers final: 29 residues processed: 154 average time/residue: 0.4773 time to fit residues: 87.4374 Evaluate side-chains 152 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 201 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.139214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098081 restraints weight = 33813.081| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.12 r_work: 0.3136 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21871 Z= 0.235 Angle : 0.626 9.491 29908 Z= 0.319 Chirality : 0.047 0.197 3605 Planarity : 0.005 0.053 3804 Dihedral : 5.202 44.378 3593 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.85 % Allowed : 13.05 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2750 helix: 2.23 (0.21), residues: 660 sheet: -0.46 (0.19), residues: 628 loop : -1.10 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 646 TYR 0.022 0.002 TYR B1067 PHE 0.035 0.002 PHE A 643 TRP 0.019 0.002 TRP C 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00558 (21807) covalent geometry : angle 0.60975 (29750) SS BOND : bond 0.00443 ( 34) SS BOND : angle 1.25579 ( 68) hydrogen bonds : bond 0.05057 ( 1007) hydrogen bonds : angle 5.88841 ( 2733) link_BETA1-4 : bond 0.00366 ( 10) link_BETA1-4 : angle 1.52990 ( 30) link_NAG-ASN : bond 0.00522 ( 20) link_NAG-ASN : angle 2.82416 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4387 (m-40) cc_final: 0.4086 (p0) REVERT: A 64 TRP cc_start: 0.6643 (t60) cc_final: 0.6324 (t60) REVERT: A 697 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9034 (ptt) REVERT: A 994 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: B 203 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7730 (pt) REVERT: B 607 GLN cc_start: 0.8232 (tt0) cc_final: 0.7846 (mm-40) REVERT: B 619 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: B 964 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8212 (mppt) REVERT: C 957 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7843 (tp40) outliers start: 40 outliers final: 29 residues processed: 146 average time/residue: 0.4785 time to fit residues: 82.7800 Evaluate side-chains 142 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 71 optimal weight: 1.9990 chunk 187 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 218 optimal weight: 0.0000 chunk 156 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 242 optimal weight: 0.9990 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1135 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104424 restraints weight = 33767.405| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.13 r_work: 0.3176 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 21871 Z= 0.108 Angle : 0.532 12.017 29908 Z= 0.273 Chirality : 0.043 0.179 3605 Planarity : 0.004 0.061 3804 Dihedral : 4.640 38.533 3593 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 13.75 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2750 helix: 2.45 (0.21), residues: 671 sheet: -0.31 (0.19), residues: 664 loop : -1.00 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 646 TYR 0.023 0.001 TYR A 423 PHE 0.034 0.001 PHE A 643 TRP 0.012 0.001 TRP A 436 HIS 0.002 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00241 (21807) covalent geometry : angle 0.51717 (29750) SS BOND : bond 0.00287 ( 34) SS BOND : angle 1.41932 ( 68) hydrogen bonds : bond 0.03953 ( 1007) hydrogen bonds : angle 5.53744 ( 2733) link_BETA1-4 : bond 0.00462 ( 10) link_BETA1-4 : angle 1.10805 ( 30) link_NAG-ASN : bond 0.00309 ( 20) link_NAG-ASN : angle 2.32821 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7120.76 seconds wall clock time: 121 minutes 58.23 seconds (7318.23 seconds total)