Starting phenix.real_space_refine on Thu Oct 29 00:35:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9smk_55036/10_2026/9smk_55036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9smk_55036/10_2026/9smk_55036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9smk_55036/10_2026/9smk_55036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9smk_55036/10_2026/9smk_55036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9smk_55036/10_2026/9smk_55036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9smk_55036/10_2026/9smk_55036.map" } resolution = 3.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 19268 2.51 5 N 5148 2.21 5 O 5144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29716 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, D Time building chain proxies: 15.69, per 1000 atoms: 0.53 Number of scatterers: 29716 At special positions: 0 Unit cell: (138.475, 137.025, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 5144 8.00 N 5148 7.00 C 19268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6896 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 70.0% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.810A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 161 through 177 removed outlier: 3.723A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.321A pdb=" N SER A 206 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.399A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 4.193A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.581A pdb=" N ARG A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.936A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.511A pdb=" N ASN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.037A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.590A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 471 through 481 removed outlier: 3.988A pdb=" N ASN A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 606 through 634 removed outlier: 3.922A pdb=" N ALA A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.561A pdb=" N LEU A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.972A pdb=" N ASP A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 652' Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.793A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.704A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.617A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 778 Processing helix chain 'A' and resid 778 through 804 Processing helix chain 'A' and resid 811 through 833 removed outlier: 3.554A pdb=" N GLN A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.773A pdb=" N ARG A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.946A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.573A pdb=" N VAL A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 952 removed outlier: 4.015A pdb=" N PHE A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.653A pdb=" N PHE A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.612A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 1016 through 1031 Processing helix chain 'A' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1094 removed outlier: 3.815A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1143 Processing helix chain 'A' and resid 1143 through 1175 removed outlier: 3.904A pdb=" N HIS A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A1165 " --> pdb=" O GLN A1161 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.810A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 161 through 177 removed outlier: 3.723A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 4.321A pdb=" N SER B 206 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.399A pdb=" N ARG B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 4.193A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 316 Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.580A pdb=" N ARG B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.936A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.511A pdb=" N ASN B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 415 removed outlier: 4.037A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.590A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.638A pdb=" N ALA B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.987A pdb=" N ASN B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 606 through 634 removed outlier: 3.922A pdb=" N ALA B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.561A pdb=" N LEU B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.972A pdb=" N ASP B 651 " --> pdb=" O PRO B 647 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 647 through 652' Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.793A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.703A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.616A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 705 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 778 Processing helix chain 'B' and resid 778 through 804 Processing helix chain 'B' and resid 811 through 833 removed outlier: 3.555A pdb=" N GLN B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.774A pdb=" N ARG B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.947A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 923 removed outlier: 3.573A pdb=" N VAL B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 952 removed outlier: 4.015A pdb=" N PHE B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 974 removed outlier: 3.654A pdb=" N PHE B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.611A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 1016 through 1031 Processing helix chain 'B' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1094 removed outlier: 3.816A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1143 Processing helix chain 'B' and resid 1143 through 1175 removed outlier: 3.904A pdb=" N HIS B1164 " --> pdb=" O LYS B1160 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B1165 " --> pdb=" O GLN B1161 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B1169 " --> pdb=" O ILE B1165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN B1170 " --> pdb=" O ARG B1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.810A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 142 through 150 Processing helix chain 'C' and resid 161 through 177 removed outlier: 3.723A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 4.321A pdb=" N SER C 206 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 260 removed outlier: 4.399A pdb=" N ARG C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 4.193A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 316 Processing helix chain 'C' and resid 330 through 339 removed outlier: 3.581A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.936A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.511A pdb=" N ASN C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 415 removed outlier: 4.037A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.591A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 448 Processing helix chain 'C' and resid 456 through 465 Processing helix chain 'C' and resid 471 through 481 removed outlier: 3.987A pdb=" N ASN C 475 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 559 through 569 Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 584 through 602 Processing helix chain 'C' and resid 606 through 634 removed outlier: 3.922A pdb=" N ALA C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.561A pdb=" N LEU C 641 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 652 removed outlier: 3.972A pdb=" N ASP C 651 " --> pdb=" O PRO C 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 647 through 652' Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.794A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.703A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 705 removed outlier: 3.617A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 705 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 778 Processing helix chain 'C' and resid 778 through 804 Processing helix chain 'C' and resid 811 through 833 removed outlier: 3.554A pdb=" N GLN C 831 " --> pdb=" O GLU C 827 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 832 " --> pdb=" O GLU C 828 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 860 removed outlier: 3.774A pdb=" N ARG C 857 " --> pdb=" O SER C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.946A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 923 removed outlier: 3.574A pdb=" N VAL C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 952 removed outlier: 4.016A pdb=" N PHE C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 974 removed outlier: 3.653A pdb=" N PHE C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.612A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'C' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1094 removed outlier: 3.816A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1143 Processing helix chain 'C' and resid 1143 through 1175 removed outlier: 3.904A pdb=" N HIS C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C1165 " --> pdb=" O GLN C1161 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C1169 " --> pdb=" O ILE C1165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN C1170 " --> pdb=" O ARG C1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.810A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR D 103 " --> pdb=" O PRO D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 161 through 177 removed outlier: 3.723A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 4.321A pdb=" N SER D 206 " --> pdb=" O PRO D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 4.399A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.193A pdb=" N LEU D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.580A pdb=" N ARG D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.936A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 397 through 404 removed outlier: 3.511A pdb=" N ASN D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 415 removed outlier: 4.037A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.590A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 456 through 465 Processing helix chain 'D' and resid 471 through 481 removed outlier: 3.987A pdb=" N ASN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'D' and resid 571 through 580 Processing helix chain 'D' and resid 584 through 602 Processing helix chain 'D' and resid 606 through 634 removed outlier: 3.921A pdb=" N ALA D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.561A pdb=" N LEU D 641 " --> pdb=" O ARG D 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 removed outlier: 3.972A pdb=" N ASP D 651 " --> pdb=" O PRO D 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 647 through 652' Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.793A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.704A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 705 removed outlier: 3.617A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 705 " --> pdb=" O LEU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 778 Processing helix chain 'D' and resid 778 through 804 Processing helix chain 'D' and resid 811 through 833 removed outlier: 3.554A pdb=" N GLN D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 832 " --> pdb=" O GLU D 828 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 833 " --> pdb=" O LEU D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 860 removed outlier: 3.773A pdb=" N ARG D 857 " --> pdb=" O SER D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.947A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 923 removed outlier: 3.574A pdb=" N VAL D 923 " --> pdb=" O LYS D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 952 removed outlier: 4.015A pdb=" N PHE D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 974 removed outlier: 3.654A pdb=" N PHE D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.612A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 984 Processing helix chain 'D' and resid 1016 through 1031 Processing helix chain 'D' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1094 removed outlier: 3.815A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D1087 " --> pdb=" O SER D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1143 Processing helix chain 'D' and resid 1143 through 1175 removed outlier: 3.904A pdb=" N HIS D1164 " --> pdb=" O LYS D1160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D1165 " --> pdb=" O GLN D1161 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D1169 " --> pdb=" O ILE D1165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN D1170 " --> pdb=" O ARG D1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.027A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186 removed outlier: 5.835A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 94 removed outlier: 7.027A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 5.835A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 94 removed outlier: 7.027A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 185 through 186 removed outlier: 5.835A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 89 through 94 removed outlier: 7.028A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 186 removed outlier: 5.836A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) 1724 hydrogen bonds defined for protein. 5148 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: 6.17 Time building geometry restraints manager: 3.39 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: 5417 1.33 - 1.45: 7619 1.45 - 1.57: 17120 1.57 - 1.69: 0 1.69 - 1.81: 236 Bond restraints: 30392 Sorted by residual: bond pdb=" N GLU D 371 " pdb=" CA GLU D 371 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.86e+00 bond pdb=" N GLU B 371 " pdb=" CA GLU B 371 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.84e+00 bond pdb=" N GLU C 371 " pdb=" CA GLU C 371 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N GLU A 371 " pdb=" CA GLU A 371 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" CB TYR A1057 " pdb=" CG TYR A1057 " ideal model delta sigma weight residual 1.512 1.540 -0.028 2.20e-02 2.07e+03 1.58e+00 ... (remaining 30387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 40298 1.88 - 3.76: 805 3.76 - 5.64: 80 5.64 - 7.52: 49 7.52 - 9.39: 4 Bond angle restraints: 41236 Sorted by residual: angle pdb=" CA TYR C1057 " pdb=" CB TYR C1057 " pdb=" CG TYR C1057 " ideal model delta sigma weight residual 113.90 119.70 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA TYR A1057 " pdb=" CB TYR A1057 " pdb=" CG TYR A1057 " ideal model delta sigma weight residual 113.90 119.69 -5.79 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA TYR D1057 " pdb=" CB TYR D1057 " pdb=" CG TYR D1057 " ideal model delta sigma weight residual 113.90 119.67 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" CA TYR B1057 " pdb=" CB TYR B1057 " pdb=" CG TYR B1057 " ideal model delta sigma weight residual 113.90 119.64 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CB ARG B 287 " pdb=" CG ARG B 287 " pdb=" CD ARG B 287 " ideal model delta sigma weight residual 111.30 118.53 -7.23 2.30e+00 1.89e-01 9.89e+00 ... (remaining 41231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 16133 17.57 - 35.14: 1726 35.14 - 52.70: 573 52.70 - 70.27: 76 70.27 - 87.84: 44 Dihedral angle restraints: 18552 sinusoidal: 7876 harmonic: 10676 Sorted by residual: dihedral pdb=" CA PHE A 999 " pdb=" C PHE A 999 " pdb=" N TRP A1000 " pdb=" CA TRP A1000 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE C 999 " pdb=" C PHE C 999 " pdb=" N TRP C1000 " pdb=" CA TRP C1000 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 999 " pdb=" C PHE B 999 " pdb=" N TRP B1000 " pdb=" CA TRP B1000 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 18549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3196 0.037 - 0.074: 1189 0.074 - 0.111: 239 0.111 - 0.148: 32 0.148 - 0.185: 4 Chirality restraints: 4660 Sorted by residual: chirality pdb=" CB THR C 873 " pdb=" CA THR C 873 " pdb=" OG1 THR C 873 " pdb=" CG2 THR C 873 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB THR D 873 " pdb=" CA THR D 873 " pdb=" OG1 THR D 873 " pdb=" CG2 THR D 873 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CB THR A 873 " pdb=" CA THR A 873 " pdb=" OG1 THR A 873 " pdb=" CG2 THR A 873 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 4657 not shown) Planarity restraints: 5152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 207 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO B 208 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 207 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 208 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 207 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO C 208 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " -0.035 5.00e-02 4.00e+02 ... (remaining 5149 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 324 2.66 - 3.22: 28366 3.22 - 3.78: 47784 3.78 - 4.34: 60192 4.34 - 4.90: 98084 Nonbonded interactions: 234750 Sorted by model distance: nonbonded pdb=" OG SER B 924 " pdb=" OAH Y01 B1303 " model vdw 2.096 3.040 nonbonded pdb=" OG SER C 924 " pdb=" OAH Y01 C1304 " model vdw 2.096 3.040 nonbonded pdb=" OG SER A 924 " pdb=" OAH Y01 A1303 " model vdw 2.096 3.040 nonbonded pdb=" OG SER D 924 " pdb=" OAH Y01 D1304 " model vdw 2.096 3.040 nonbonded pdb=" O ASN A1032 " pdb=" OD1 ASN A1032 " model vdw 2.150 3.040 ... (remaining 234745 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 81 through 1175 or resid 1303 through 1304)) selection = (chain 'B' and (resid 81 through 1175 or resid 1303 through 1304)) selection = (chain 'C' and (resid 81 through 1175 or resid 1303 through 1304)) selection = (chain 'D' and (resid 81 through 1175 or resid 1303 through 1304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.430 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: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 36.000 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30396 Z= 0.152 Angle : 0.639 9.394 41244 Z= 0.317 Chirality : 0.038 0.185 4660 Planarity : 0.005 0.064 5152 Dihedral : 16.407 87.838 11644 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.13 % Allowed : 26.31 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.15), residues: 3640 helix: 1.44 (0.11), residues: 2412 sheet: -2.95 (0.41), residues: 140 loop : -2.52 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 632 TYR 0.020 0.002 TYR C1057 PHE 0.017 0.002 PHE B 440 TRP 0.013 0.002 TRP A 649 HIS 0.003 0.001 HIS D 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (30392) covalent geometry : angle 0.63876 / 0.32 (41236) SS BOND : bond 0.00257 / 0.12 ( 4) SS BOND : angle 0.19335 / 0.10 ( 8) hydrogen bonds : bond 0.09431 / 6.63 ( 1724) hydrogen bonds : angle 4.41186 / 3.13 ( 5148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 445 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.6124 (t80) REVERT: A 641 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7462 (tt) REVERT: A 817 LEU cc_start: 0.8264 (tp) cc_final: 0.7998 (tt) REVERT: B 464 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.5949 (t80) REVERT: B 641 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7443 (tt) REVERT: B 817 LEU cc_start: 0.8163 (tp) cc_final: 0.7893 (tt) REVERT: C 464 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.6011 (t80) REVERT: C 641 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7450 (tt) REVERT: C 817 LEU cc_start: 0.8165 (tp) cc_final: 0.7926 (tt) REVERT: D 464 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.6161 (t80) REVERT: D 622 MET cc_start: 0.5739 (ttp) cc_final: 0.5156 (ttm) REVERT: D 641 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7485 (tt) REVERT: D 817 LEU cc_start: 0.8281 (tp) cc_final: 0.8019 (tt) outliers start: 65 outliers final: 20 residues processed: 501 average time/residue: 0.1948 time to fit residues: 151.4400 Evaluate side-chains 283 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 464 TYR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 464 TYR Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 987 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 424 HIS ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 HIS A1014 GLN A1061 GLN B 419 GLN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 HIS B1014 GLN B1061 GLN B1170 GLN C 419 GLN C 424 HIS ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 HIS C1014 GLN C1037 ASN C1061 GLN D 419 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 889 HIS D1014 GLN D1037 ASN D1061 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.067324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051628 restraints weight = 164998.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053009 restraints weight = 101482.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053894 restraints weight = 73498.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054534 restraints weight = 59513.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054785 restraints weight = 51296.951| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 30396 Z= 0.352 Angle : 0.786 9.189 41244 Z= 0.396 Chirality : 0.043 0.181 4660 Planarity : 0.006 0.065 5152 Dihedral : 7.973 57.167 4976 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 8.62 % Allowed : 20.48 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.09 (0.14), residues: 3640 helix: 1.38 (0.11), residues: 2460 sheet: -3.65 (0.30), residues: 192 loop : -2.59 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 334 TYR 0.015 0.002 TYR B 229 PHE 0.025 0.002 PHE C 627 TRP 0.013 0.002 TRP C 776 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.35 (30392) covalent geometry : angle 0.78622 / 0.40 (41236) SS BOND : bond 0.00312 / 0.15 ( 4) SS BOND : angle 0.31363 / 0.18 ( 8) hydrogen bonds : bond 0.03943 / 2.67 ( 1724) hydrogen bonds : angle 4.43898 / 3.18 ( 5148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 248 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8906 (mt) REVERT: A 414 PHE cc_start: 0.8749 (t80) cc_final: 0.8499 (t80) REVERT: A 562 LEU cc_start: 0.9794 (OUTLIER) cc_final: 0.9559 (tp) REVERT: A 641 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9418 (tt) REVERT: A 817 LEU cc_start: 0.9773 (tp) cc_final: 0.9453 (tt) REVERT: A 1154 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.8880 (ptmm) REVERT: A 1156 ASP cc_start: 0.9218 (m-30) cc_final: 0.8877 (m-30) REVERT: A 1168 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.6618 (t80) REVERT: B 449 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8121 (mm) REVERT: B 562 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9531 (tp) REVERT: B 580 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8783 (mt-10) REVERT: B 641 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9418 (tt) REVERT: B 817 LEU cc_start: 0.9768 (tp) cc_final: 0.9441 (tt) REVERT: B 1146 GLU cc_start: 0.9462 (tp30) cc_final: 0.8851 (tp30) REVERT: B 1154 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9171 (ttpp) REVERT: B 1168 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.6776 (t80) REVERT: C 449 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 562 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9544 (tp) REVERT: C 580 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8838 (mt-10) REVERT: C 641 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9415 (tt) REVERT: C 792 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9573 (mm) REVERT: C 817 LEU cc_start: 0.9773 (tp) cc_final: 0.9453 (tt) REVERT: C 1146 GLU cc_start: 0.9447 (tp30) cc_final: 0.8838 (tp30) REVERT: C 1154 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9199 (ptmm) REVERT: C 1168 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6469 (t80) REVERT: D 376 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8872 (mt) REVERT: D 449 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8227 (mm) REVERT: D 562 LEU cc_start: 0.9794 (OUTLIER) cc_final: 0.9560 (tp) REVERT: D 580 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8742 (mt-10) REVERT: D 641 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9419 (tt) REVERT: D 708 ILE cc_start: 0.8479 (tt) cc_final: 0.7692 (tt) REVERT: D 792 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9569 (mm) REVERT: D 817 LEU cc_start: 0.9777 (tp) cc_final: 0.9456 (tt) REVERT: D 1154 LYS cc_start: 0.9678 (OUTLIER) cc_final: 0.9303 (ptmm) REVERT: D 1156 ASP cc_start: 0.9221 (m-30) cc_final: 0.8942 (m-30) REVERT: D 1168 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.6443 (t80) outliers start: 263 outliers final: 110 residues processed: 474 average time/residue: 0.1535 time to fit residues: 123.0023 Evaluate side-chains 355 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 222 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 939 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1154 LYS Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [335, 157, 17, 180, 272, 118, 69, 6, 65, 303, 30] chunk 335 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 303 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 GLN A 410 GLN ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 410 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052421 restraints weight = 164052.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053872 restraints weight = 98062.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054828 restraints weight = 70019.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055481 restraints weight = 55846.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055731 restraints weight = 47967.909| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30396 Z= 0.181 Angle : 0.654 10.770 41244 Z= 0.320 Chirality : 0.039 0.156 4660 Planarity : 0.005 0.055 5152 Dihedral : 7.590 59.113 4950 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.87 % Allowed : 23.89 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.30 (0.14), residues: 3640 helix: 1.56 (0.11), residues: 2448 sheet: -3.28 (0.36), residues: 148 loop : -2.66 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 405 TYR 0.012 0.001 TYR B 211 PHE 0.017 0.001 PHE D 627 TRP 0.011 0.002 TRP A1000 HIS 0.003 0.001 HIS D1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (30392) covalent geometry : angle 0.65439 / 0.32 (41236) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 0.04753 / 0.03 ( 8) hydrogen bonds : bond 0.03579 / 2.42 ( 1724) hydrogen bonds : angle 4.19350 / 3.00 ( 5148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 241 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8959 (mt) REVERT: A 414 PHE cc_start: 0.8628 (t80) cc_final: 0.8359 (t80) REVERT: A 562 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9537 (tp) REVERT: A 580 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8778 (mt-10) REVERT: A 641 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9420 (tt) REVERT: A 784 MET cc_start: 0.9087 (tpt) cc_final: 0.8861 (tpt) REVERT: A 1154 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9172 (ptmm) REVERT: A 1156 ASP cc_start: 0.9230 (m-30) cc_final: 0.8863 (m-30) REVERT: A 1168 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.6454 (t80) REVERT: A 1170 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8770 (pp30) REVERT: B 562 LEU cc_start: 0.9760 (OUTLIER) cc_final: 0.9524 (tp) REVERT: B 580 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8701 (mt-10) REVERT: B 641 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9429 (tt) REVERT: B 784 MET cc_start: 0.9086 (tpt) cc_final: 0.8862 (tpt) REVERT: B 1146 GLU cc_start: 0.9441 (tp30) cc_final: 0.8836 (tp30) REVERT: B 1154 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9083 (ttpp) REVERT: B 1168 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.6740 (t80) REVERT: C 376 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8936 (mt) REVERT: C 562 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9527 (tp) REVERT: C 580 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8757 (mt-10) REVERT: C 641 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9422 (tt) REVERT: C 784 MET cc_start: 0.9084 (tpt) cc_final: 0.8861 (tpt) REVERT: C 792 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9569 (mm) REVERT: C 1146 GLU cc_start: 0.9441 (tp30) cc_final: 0.8861 (tp30) REVERT: C 1154 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9122 (ttpp) REVERT: C 1168 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.6640 (t80) REVERT: D 376 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8940 (mt) REVERT: D 562 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9534 (tp) REVERT: D 580 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8667 (mt-10) REVERT: D 641 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9417 (tt) REVERT: D 784 MET cc_start: 0.9084 (tpt) cc_final: 0.8851 (tpt) REVERT: D 1156 ASP cc_start: 0.9233 (m-30) cc_final: 0.8938 (m-30) REVERT: D 1168 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.6615 (t80) outliers start: 179 outliers final: 96 residues processed: 388 average time/residue: 0.1607 time to fit residues: 104.9049 Evaluate side-chains 342 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 227 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1040 ILE Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [263, 228, 244, 54, 214, 365, 113, 198, 112, 105, 118] chunk 263 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 214 optimal weight: 30.0000 chunk 365 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 424 HIS ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049280 restraints weight = 166414.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.050633 restraints weight = 100553.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051550 restraints weight = 71519.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052172 restraints weight = 57381.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052583 restraints weight = 49093.980| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30396 Z= 0.277 Angle : 0.708 7.722 41244 Z= 0.356 Chirality : 0.040 0.165 4660 Planarity : 0.005 0.056 5152 Dihedral : 7.493 59.564 4950 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.52 % Allowed : 23.33 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.14), residues: 3640 helix: 1.45 (0.11), residues: 2464 sheet: -3.65 (0.30), residues: 192 loop : -2.52 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 612 TYR 0.016 0.002 TYR C1063 PHE 0.020 0.002 PHE D 627 TRP 0.017 0.002 TRP D 152 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (30392) covalent geometry : angle 0.70790 / 0.36 (41236) SS BOND : bond 0.00206 / 0.10 ( 4) SS BOND : angle 0.18448 / 0.10 ( 8) hydrogen bonds : bond 0.03787 / 2.56 ( 1724) hydrogen bonds : angle 4.35789 / 3.12 ( 5148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 221 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8886 (mtt) cc_final: 0.8635 (mtt) REVERT: A 186 MET cc_start: 0.8290 (mmm) cc_final: 0.7923 (mmp) REVERT: A 284 MET cc_start: 0.8167 (mmt) cc_final: 0.7634 (mmp) REVERT: A 410 GLN cc_start: 0.9625 (tp-100) cc_final: 0.9347 (tp-100) REVERT: A 562 LEU cc_start: 0.9795 (OUTLIER) cc_final: 0.9554 (tp) REVERT: A 580 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8750 (mp0) REVERT: A 641 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9362 (tt) REVERT: A 675 LEU cc_start: 0.9593 (tp) cc_final: 0.9385 (tt) REVERT: A 1168 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.6796 (t80) REVERT: A 1170 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8814 (pp30) REVERT: B 175 MET cc_start: 0.8846 (mtt) cc_final: 0.8616 (mtt) REVERT: B 186 MET cc_start: 0.8475 (mmm) cc_final: 0.8055 (mmp) REVERT: B 410 GLN cc_start: 0.9600 (tp-100) cc_final: 0.9307 (tp-100) REVERT: B 414 PHE cc_start: 0.8594 (t80) cc_final: 0.8302 (t80) REVERT: B 562 LEU cc_start: 0.9787 (OUTLIER) cc_final: 0.9535 (tp) REVERT: B 580 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8706 (mp0) REVERT: B 641 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9373 (tt) REVERT: B 675 LEU cc_start: 0.9583 (tp) cc_final: 0.9368 (tt) REVERT: B 1146 GLU cc_start: 0.9423 (tp30) cc_final: 0.8813 (tp30) REVERT: B 1168 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 186 MET cc_start: 0.8377 (mmm) cc_final: 0.8009 (mmp) REVERT: C 410 GLN cc_start: 0.9602 (tp-100) cc_final: 0.9308 (tp-100) REVERT: C 414 PHE cc_start: 0.8593 (t80) cc_final: 0.8296 (t80) REVERT: C 562 LEU cc_start: 0.9788 (OUTLIER) cc_final: 0.9538 (tp) REVERT: C 580 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8769 (mp0) REVERT: C 641 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9373 (tt) REVERT: C 675 LEU cc_start: 0.9581 (tp) cc_final: 0.9368 (tt) REVERT: C 1146 GLU cc_start: 0.9418 (tp30) cc_final: 0.8813 (tp30) REVERT: C 1154 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9134 (ptmm) REVERT: C 1168 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.6766 (t80) REVERT: D 175 MET cc_start: 0.8881 (mtt) cc_final: 0.8630 (mtt) REVERT: D 186 MET cc_start: 0.8473 (mmm) cc_final: 0.8110 (mmp) REVERT: D 410 GLN cc_start: 0.9622 (tp-100) cc_final: 0.9278 (tp-100) REVERT: D 414 PHE cc_start: 0.8604 (t80) cc_final: 0.8273 (t80) REVERT: D 562 LEU cc_start: 0.9795 (OUTLIER) cc_final: 0.9548 (tp) REVERT: D 580 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8626 (mp0) REVERT: D 641 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9363 (tt) REVERT: D 675 LEU cc_start: 0.9592 (tp) cc_final: 0.9386 (tt) REVERT: D 1154 LYS cc_start: 0.9642 (OUTLIER) cc_final: 0.9288 (ptmm) REVERT: D 1168 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.6726 (t80) outliers start: 199 outliers final: 111 residues processed: 396 average time/residue: 0.1505 time to fit residues: 102.0630 Evaluate side-chains 330 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 205 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1150 ARG Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1154 LYS Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [56, 154, 86, 71, 244, 257, 24, 273, 348, 136, 146] chunk 56 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 348 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 669 GLN ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.067119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051728 restraints weight = 164469.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053145 restraints weight = 96694.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054117 restraints weight = 68591.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054712 restraints weight = 54575.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055171 restraints weight = 47440.390| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30396 Z= 0.118 Angle : 0.636 9.698 41244 Z= 0.306 Chirality : 0.038 0.172 4660 Planarity : 0.005 0.054 5152 Dihedral : 7.470 59.689 4950 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.59 % Allowed : 23.59 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.51 (0.14), residues: 3640 helix: 1.64 (0.11), residues: 2472 sheet: -2.91 (0.44), residues: 92 loop : -2.59 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 459 TYR 0.016 0.001 TYR A 393 PHE 0.025 0.001 PHE A 414 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS D 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (30392) covalent geometry : angle 0.63560 / 0.31 (41236) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 0.18880 / 0.10 ( 8) hydrogen bonds : bond 0.03353 / 2.28 ( 1724) hydrogen bonds : angle 4.07464 / 2.94 ( 5148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 238 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8849 (mtt) cc_final: 0.8591 (mtt) REVERT: A 284 MET cc_start: 0.8093 (mmt) cc_final: 0.7653 (mmp) REVERT: A 410 GLN cc_start: 0.9614 (tp-100) cc_final: 0.9276 (tp-100) REVERT: A 414 PHE cc_start: 0.8526 (t80) cc_final: 0.8250 (t80) REVERT: A 562 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9524 (tp) REVERT: A 576 MET cc_start: 0.9367 (tpp) cc_final: 0.9018 (mmm) REVERT: A 580 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8659 (mp0) REVERT: A 641 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9342 (tt) REVERT: A 675 LEU cc_start: 0.9568 (tp) cc_final: 0.9367 (tt) REVERT: A 1156 ASP cc_start: 0.9090 (m-30) cc_final: 0.8745 (m-30) REVERT: A 1170 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8824 (pp30) REVERT: B 186 MET cc_start: 0.8476 (mmm) cc_final: 0.8030 (mmp) REVERT: B 313 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8676 (pt0) REVERT: B 410 GLN cc_start: 0.9603 (tp-100) cc_final: 0.9305 (tp-100) REVERT: B 414 PHE cc_start: 0.8542 (t80) cc_final: 0.8276 (t80) REVERT: B 562 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9518 (tp) REVERT: B 576 MET cc_start: 0.9316 (tpp) cc_final: 0.9040 (mmm) REVERT: B 580 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8602 (mp0) REVERT: B 641 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9344 (tt) REVERT: B 675 LEU cc_start: 0.9564 (tp) cc_final: 0.9360 (tt) REVERT: B 936 PHE cc_start: 0.9204 (t80) cc_final: 0.8967 (t80) REVERT: B 1038 LEU cc_start: 0.9709 (tt) cc_final: 0.9497 (tp) REVERT: B 1146 GLU cc_start: 0.9383 (tp30) cc_final: 0.8778 (tp30) REVERT: C 186 MET cc_start: 0.8353 (mmm) cc_final: 0.7937 (mmp) REVERT: C 284 MET cc_start: 0.8030 (mmt) cc_final: 0.7562 (mmp) REVERT: C 313 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8694 (pt0) REVERT: C 410 GLN cc_start: 0.9596 (tp-100) cc_final: 0.9271 (tp-100) REVERT: C 414 PHE cc_start: 0.8535 (t80) cc_final: 0.8244 (t80) REVERT: C 562 LEU cc_start: 0.9760 (OUTLIER) cc_final: 0.9525 (tp) REVERT: C 576 MET cc_start: 0.9401 (tpp) cc_final: 0.9012 (mmm) REVERT: C 580 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8643 (mp0) REVERT: C 641 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9353 (tt) REVERT: C 675 LEU cc_start: 0.9563 (tp) cc_final: 0.9362 (tt) REVERT: C 1146 GLU cc_start: 0.9386 (tp30) cc_final: 0.8776 (tp30) REVERT: D 175 MET cc_start: 0.8824 (mtt) cc_final: 0.8562 (mtt) REVERT: D 186 MET cc_start: 0.8440 (mmm) cc_final: 0.8097 (mmp) REVERT: D 284 MET cc_start: 0.8055 (mmt) cc_final: 0.7620 (mmp) REVERT: D 410 GLN cc_start: 0.9599 (tp-100) cc_final: 0.9305 (tp-100) REVERT: D 562 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9526 (tp) REVERT: D 580 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8587 (mt-10) REVERT: D 613 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9289 (mmtm) REVERT: D 641 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9345 (tt) REVERT: D 675 LEU cc_start: 0.9576 (tp) cc_final: 0.9375 (tt) REVERT: D 1156 ASP cc_start: 0.8753 (m-30) cc_final: 0.8531 (m-30) REVERT: D 1168 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7191 (t80) outliers start: 140 outliers final: 84 residues processed: 364 average time/residue: 0.1530 time to fit residues: 95.1048 Evaluate side-chains 316 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 220 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 953 ARG Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1150 ARG Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 613 LYS Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 953 ARG Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [296, 20, 354, 6, 32, 116, 50, 7, 224, 332, 122] chunk 296 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 354 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 332 optimal weight: 0.2980 chunk 122 optimal weight: 6.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A1037 ASN B 260 GLN B1037 ASN C1037 ASN D1037 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.066279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051038 restraints weight = 165812.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052464 restraints weight = 97566.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053291 restraints weight = 68991.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053984 restraints weight = 55984.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054477 restraints weight = 47987.408| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30396 Z= 0.141 Angle : 0.614 7.583 41244 Z= 0.301 Chirality : 0.037 0.167 4660 Planarity : 0.005 0.110 5152 Dihedral : 7.381 59.233 4950 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.95 % Allowed : 23.46 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.60 (0.15), residues: 3640 helix: 1.71 (0.11), residues: 2472 sheet: -2.83 (0.39), residues: 140 loop : -2.51 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 437 TYR 0.009 0.001 TYR A 393 PHE 0.023 0.001 PHE D 414 TRP 0.015 0.001 TRP A 152 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (30392) covalent geometry : angle 0.61435 / 0.30 (41236) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 0.19333 / 0.11 ( 8) hydrogen bonds : bond 0.03295 / 2.23 ( 1724) hydrogen bonds : angle 4.06136 / 2.93 ( 5148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 225 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8164 (mmm) cc_final: 0.7536 (mmt) REVERT: A 284 MET cc_start: 0.8154 (mmt) cc_final: 0.7725 (mmp) REVERT: A 410 GLN cc_start: 0.9618 (tp-100) cc_final: 0.9343 (tp-100) REVERT: A 562 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9519 (tp) REVERT: A 576 MET cc_start: 0.9359 (tpp) cc_final: 0.9003 (mmm) REVERT: A 580 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8700 (mp0) REVERT: A 641 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9333 (tt) REVERT: A 675 LEU cc_start: 0.9575 (tp) cc_final: 0.9370 (tt) REVERT: A 1156 ASP cc_start: 0.9089 (m-30) cc_final: 0.8742 (m-30) REVERT: A 1168 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.6464 (t80) REVERT: A 1170 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8853 (pp30) REVERT: B 186 MET cc_start: 0.8448 (mmm) cc_final: 0.8097 (mmt) REVERT: B 313 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: B 394 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8817 (mt) REVERT: B 410 GLN cc_start: 0.9579 (tp-100) cc_final: 0.9324 (tp-100) REVERT: B 562 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9517 (tp) REVERT: B 576 MET cc_start: 0.9291 (tpp) cc_final: 0.8997 (mmm) REVERT: B 580 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8666 (mp0) REVERT: B 641 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9347 (tt) REVERT: B 675 LEU cc_start: 0.9573 (tp) cc_final: 0.9371 (tt) REVERT: B 1038 LEU cc_start: 0.9690 (tt) cc_final: 0.9448 (tp) REVERT: B 1146 GLU cc_start: 0.9384 (tp30) cc_final: 0.8791 (tp30) REVERT: B 1168 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.6779 (t80) REVERT: C 284 MET cc_start: 0.8086 (mmt) cc_final: 0.7639 (mmp) REVERT: C 313 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: C 410 GLN cc_start: 0.9582 (tp-100) cc_final: 0.9328 (tp-100) REVERT: C 562 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9512 (tp) REVERT: C 576 MET cc_start: 0.9371 (tpp) cc_final: 0.9031 (mmm) REVERT: C 580 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8700 (mp0) REVERT: C 641 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9336 (tt) REVERT: C 675 LEU cc_start: 0.9573 (tp) cc_final: 0.9372 (tt) REVERT: C 684 MET cc_start: 0.8278 (mmt) cc_final: 0.7890 (tpp) REVERT: C 1146 GLU cc_start: 0.9384 (tp30) cc_final: 0.8776 (tp30) REVERT: C 1168 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.6633 (t80) REVERT: D 186 MET cc_start: 0.8444 (mmm) cc_final: 0.8181 (mmt) REVERT: D 284 MET cc_start: 0.8130 (mmt) cc_final: 0.7713 (mmp) REVERT: D 410 GLN cc_start: 0.9609 (tp-100) cc_final: 0.9332 (tp-100) REVERT: D 562 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9524 (tp) REVERT: D 580 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8712 (mt-10) REVERT: D 641 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9336 (tt) REVERT: D 675 LEU cc_start: 0.9585 (tp) cc_final: 0.9382 (tt) REVERT: D 1168 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.6908 (t80) outliers start: 151 outliers final: 92 residues processed: 358 average time/residue: 0.1510 time to fit residues: 93.0974 Evaluate side-chains 321 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 214 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1150 ARG Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [271, 118, 305, 113, 333, 65, 44, 193, 5, 213, 251] chunk 271 optimal weight: 0.5980 chunk 118 optimal weight: 20.0000 chunk 305 optimal weight: 0.0020 chunk 113 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN D 260 GLN ** D1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.066512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.051415 restraints weight = 165853.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052817 restraints weight = 97042.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.053810 restraints weight = 68435.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054480 restraints weight = 54325.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.054743 restraints weight = 46265.163| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30396 Z= 0.124 Angle : 0.619 10.438 41244 Z= 0.299 Chirality : 0.037 0.178 4660 Planarity : 0.005 0.053 5152 Dihedral : 7.336 58.861 4950 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.42 % Allowed : 24.74 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.66 (0.15), residues: 3640 helix: 1.80 (0.11), residues: 2456 sheet: -2.77 (0.40), residues: 140 loop : -2.56 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 892 TYR 0.009 0.001 TYR D 256 PHE 0.024 0.001 PHE C 414 TRP 0.015 0.001 TRP A 152 HIS 0.002 0.000 HIS D1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (30392) covalent geometry : angle 0.61884 / 0.30 (41236) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.19116 / 0.11 ( 8) hydrogen bonds : bond 0.03151 / 2.13 ( 1724) hydrogen bonds : angle 3.99954 / 2.89 ( 5148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 224 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8727 (mtt) cc_final: 0.8423 (mmt) REVERT: A 186 MET cc_start: 0.8261 (mmm) cc_final: 0.8025 (mmm) REVERT: A 284 MET cc_start: 0.8128 (mmt) cc_final: 0.7753 (mmp) REVERT: A 410 GLN cc_start: 0.9616 (tp-100) cc_final: 0.9351 (tp-100) REVERT: A 562 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9512 (tp) REVERT: A 576 MET cc_start: 0.9357 (tpp) cc_final: 0.9020 (mmm) REVERT: A 580 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8693 (mp0) REVERT: A 641 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9313 (tt) REVERT: A 684 MET cc_start: 0.8158 (mmt) cc_final: 0.7587 (tpp) REVERT: A 1153 GLN cc_start: 0.8959 (pp30) cc_final: 0.8656 (pp30) REVERT: A 1156 ASP cc_start: 0.9079 (m-30) cc_final: 0.8717 (m-30) REVERT: A 1168 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.6604 (t80) REVERT: A 1170 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8842 (pp30) REVERT: B 186 MET cc_start: 0.8479 (mmm) cc_final: 0.8168 (mmt) REVERT: B 284 MET cc_start: 0.8041 (mmt) cc_final: 0.7593 (mmp) REVERT: B 313 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: B 394 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8795 (mt) REVERT: B 410 GLN cc_start: 0.9583 (tp-100) cc_final: 0.9274 (tp-100) REVERT: B 414 PHE cc_start: 0.8551 (t80) cc_final: 0.8288 (t80) REVERT: B 562 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9374 (tp) REVERT: B 576 MET cc_start: 0.9296 (tpp) cc_final: 0.8988 (mmm) REVERT: B 580 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8666 (mp0) REVERT: B 641 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9329 (tt) REVERT: B 684 MET cc_start: 0.8258 (tpp) cc_final: 0.7824 (tpp) REVERT: B 1146 GLU cc_start: 0.9370 (tp30) cc_final: 0.8782 (tp30) REVERT: B 1168 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.6869 (t80) REVERT: C 186 MET cc_start: 0.8125 (mmm) cc_final: 0.7606 (mmm) REVERT: C 284 MET cc_start: 0.8103 (mmt) cc_final: 0.7669 (mmp) REVERT: C 313 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8745 (pt0) REVERT: C 410 GLN cc_start: 0.9587 (tp-100) cc_final: 0.9280 (tp-100) REVERT: C 414 PHE cc_start: 0.8560 (t80) cc_final: 0.8290 (t80) REVERT: C 562 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9379 (tp) REVERT: C 576 MET cc_start: 0.9344 (tpp) cc_final: 0.8991 (mmm) REVERT: C 580 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8686 (mp0) REVERT: C 641 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9323 (tt) REVERT: C 684 MET cc_start: 0.8277 (mmt) cc_final: 0.8066 (tpp) REVERT: C 1146 GLU cc_start: 0.9376 (tp30) cc_final: 0.8764 (tp30) REVERT: C 1168 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.6684 (t80) REVERT: D 175 MET cc_start: 0.8722 (mtt) cc_final: 0.8419 (mmt) REVERT: D 186 MET cc_start: 0.8478 (mmm) cc_final: 0.8177 (mmt) REVERT: D 284 MET cc_start: 0.8128 (mmt) cc_final: 0.7716 (mmp) REVERT: D 410 GLN cc_start: 0.9610 (tp-100) cc_final: 0.9344 (tp-100) REVERT: D 562 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9521 (tp) REVERT: D 580 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8687 (mt-10) REVERT: D 641 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9312 (tt) REVERT: D 1156 ASP cc_start: 0.9013 (m-30) cc_final: 0.8660 (m-30) REVERT: D 1168 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.6957 (t80) outliers start: 135 outliers final: 98 residues processed: 343 average time/residue: 0.1488 time to fit residues: 88.2792 Evaluate side-chains 331 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 218 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1150 ARG Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [40, 130, 34, 114, 15, 87, 51, 260, 268, 267, 321] chunk 40 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 0.0050 chunk 260 optimal weight: 6.9990 chunk 268 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 321 optimal weight: 9.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1153 GLN ** 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 = 0.3513 r_free = 0.3513 target = 0.066072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050868 restraints weight = 168447.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.052318 restraints weight = 99142.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053281 restraints weight = 69890.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053933 restraints weight = 55388.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.054179 restraints weight = 47417.934| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30396 Z= 0.136 Angle : 0.620 13.311 41244 Z= 0.300 Chirality : 0.037 0.200 4660 Planarity : 0.005 0.053 5152 Dihedral : 7.279 58.009 4950 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.46 % Allowed : 25.16 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.76 (0.15), residues: 3640 helix: 1.88 (0.11), residues: 2456 sheet: -2.71 (0.40), residues: 140 loop : -2.54 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 953 TYR 0.009 0.001 TYR D 256 PHE 0.023 0.001 PHE A 414 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS B1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (30392) covalent geometry : angle 0.62048 / 0.30 (41236) SS BOND : bond 0.00151 / 0.07 ( 4) SS BOND : angle 0.08061 / 0.04 ( 8) hydrogen bonds : bond 0.03142 / 2.13 ( 1724) hydrogen bonds : angle 3.97772 / 2.87 ( 5148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 219 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.8165 (mmt) cc_final: 0.7783 (mmp) REVERT: A 410 GLN cc_start: 0.9614 (tp-100) cc_final: 0.9361 (tp-100) REVERT: A 562 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9505 (tp) REVERT: A 576 MET cc_start: 0.9408 (tpp) cc_final: 0.9049 (mmm) REVERT: A 580 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8719 (mp0) REVERT: A 641 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9324 (tt) REVERT: A 1153 GLN cc_start: 0.8957 (pp30) cc_final: 0.8655 (pp30) REVERT: A 1156 ASP cc_start: 0.9110 (m-30) cc_final: 0.8749 (m-30) REVERT: A 1168 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 1170 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8886 (pp30) REVERT: B 284 MET cc_start: 0.8079 (mmt) cc_final: 0.7648 (mmp) REVERT: B 313 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: B 410 GLN cc_start: 0.9587 (tp-100) cc_final: 0.9272 (tp-100) REVERT: B 414 PHE cc_start: 0.8597 (t80) cc_final: 0.8337 (t80) REVERT: B 562 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9409 (tp) REVERT: B 580 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8678 (mt-10) REVERT: B 641 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9336 (tt) REVERT: B 684 MET cc_start: 0.8191 (tpp) cc_final: 0.7962 (tpp) REVERT: B 988 MET cc_start: 0.7995 (ttp) cc_final: 0.7249 (ptm) REVERT: B 1150 ARG cc_start: 0.9474 (OUTLIER) cc_final: 0.8878 (mtm110) REVERT: C 186 MET cc_start: 0.8210 (mmm) cc_final: 0.7940 (mmm) REVERT: C 225 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7642 (mm) REVERT: C 284 MET cc_start: 0.8123 (mmt) cc_final: 0.7708 (mmp) REVERT: C 410 GLN cc_start: 0.9588 (tp-100) cc_final: 0.9276 (tp-100) REVERT: C 414 PHE cc_start: 0.8590 (t80) cc_final: 0.8346 (t80) REVERT: C 562 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9393 (tp) REVERT: C 576 MET cc_start: 0.9412 (tpp) cc_final: 0.9005 (mmm) REVERT: C 580 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8688 (mp0) REVERT: C 641 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9319 (tt) REVERT: C 1146 GLU cc_start: 0.9372 (tp30) cc_final: 0.8758 (tp30) REVERT: C 1156 ASP cc_start: 0.8897 (m-30) cc_final: 0.8565 (m-30) REVERT: D 284 MET cc_start: 0.8155 (mmt) cc_final: 0.7788 (mmp) REVERT: D 410 GLN cc_start: 0.9605 (tp-100) cc_final: 0.9294 (tp-100) REVERT: D 562 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9507 (tp) REVERT: D 580 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8692 (mt-10) REVERT: D 641 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9329 (tt) REVERT: D 1156 ASP cc_start: 0.8993 (m-30) cc_final: 0.8622 (m-30) REVERT: D 1168 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7523 (t80) outliers start: 136 outliers final: 99 residues processed: 342 average time/residue: 0.1490 time to fit residues: 89.6931 Evaluate side-chains 327 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 215 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1150 ARG Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [67, 302, 303, 187, 77, 238, 150, 220, 252, 331, 35] chunk 67 optimal weight: 1.9990 chunk 302 optimal weight: 30.0000 chunk 303 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 chunk 331 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1153 GLN ** 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 = 0.3533 r_free = 0.3533 target = 0.066709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051788 restraints weight = 162746.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.053256 restraints weight = 95435.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054242 restraints weight = 66904.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054892 restraints weight = 52517.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.055380 restraints weight = 44726.196| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30396 Z= 0.112 Angle : 0.643 12.099 41244 Z= 0.304 Chirality : 0.037 0.235 4660 Planarity : 0.004 0.053 5152 Dihedral : 7.254 57.869 4948 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.77 % Allowed : 26.05 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.71 (0.15), residues: 3640 helix: 1.84 (0.11), residues: 2464 sheet: -2.77 (0.38), residues: 148 loop : -2.56 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 437 TYR 0.010 0.001 TYR B 393 PHE 0.023 0.001 PHE C 414 TRP 0.016 0.001 TRP A 152 HIS 0.002 0.000 HIS D1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (30392) covalent geometry : angle 0.64281 / 0.30 (41236) SS BOND : bond 0.00076 / 0.04 ( 4) SS BOND : angle 0.20208 / 0.11 ( 8) hydrogen bonds : bond 0.03043 / 2.07 ( 1724) hydrogen bonds : angle 3.95001 / 2.85 ( 5148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 227 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8064 (mmm) cc_final: 0.7669 (mmm) REVERT: A 284 MET cc_start: 0.8174 (mmt) cc_final: 0.7782 (mmp) REVERT: A 410 GLN cc_start: 0.9582 (tp-100) cc_final: 0.9329 (tp-100) REVERT: A 562 LEU cc_start: 0.9732 (OUTLIER) cc_final: 0.9338 (tp) REVERT: A 580 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8633 (mt-10) REVERT: A 641 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9288 (tt) REVERT: A 1153 GLN cc_start: 0.8945 (pp30) cc_final: 0.8652 (pp30) REVERT: A 1156 ASP cc_start: 0.9075 (m-30) cc_final: 0.8706 (m-30) REVERT: A 1170 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8843 (pp30) REVERT: B 186 MET cc_start: 0.8526 (mmm) cc_final: 0.7871 (mmp) REVERT: B 284 MET cc_start: 0.8053 (mmt) cc_final: 0.7606 (mmp) REVERT: B 313 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8717 (pt0) REVERT: B 410 GLN cc_start: 0.9570 (tp-100) cc_final: 0.9274 (tp-100) REVERT: B 414 PHE cc_start: 0.8533 (t80) cc_final: 0.8241 (t80) REVERT: B 562 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9380 (tp) REVERT: B 580 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8641 (mt-10) REVERT: B 641 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9297 (tt) REVERT: B 684 MET cc_start: 0.8081 (tpp) cc_final: 0.7838 (tpp) REVERT: C 186 MET cc_start: 0.8231 (mmm) cc_final: 0.7972 (mmm) REVERT: C 225 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7635 (mm) REVERT: C 284 MET cc_start: 0.8095 (mmt) cc_final: 0.7533 (ptm) REVERT: C 410 GLN cc_start: 0.9577 (tp-100) cc_final: 0.9283 (tp-100) REVERT: C 414 PHE cc_start: 0.8524 (t80) cc_final: 0.8240 (t80) REVERT: C 562 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9386 (tp) REVERT: C 580 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8629 (mt-10) REVERT: C 641 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9294 (tt) REVERT: C 1146 GLU cc_start: 0.9338 (tp30) cc_final: 0.8745 (tp30) REVERT: C 1156 ASP cc_start: 0.8887 (m-30) cc_final: 0.8550 (m-30) REVERT: C 1168 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.6836 (t80) REVERT: D 186 MET cc_start: 0.8551 (mmm) cc_final: 0.7864 (mmp) REVERT: D 284 MET cc_start: 0.8144 (mmt) cc_final: 0.7744 (mmp) REVERT: D 410 GLN cc_start: 0.9557 (tp-100) cc_final: 0.9330 (tp-100) REVERT: D 414 PHE cc_start: 0.8466 (t80) cc_final: 0.8173 (t80) REVERT: D 562 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9377 (tp) REVERT: D 580 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8650 (mt-10) REVERT: D 641 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9290 (tt) REVERT: D 1156 ASP cc_start: 0.8964 (m-30) cc_final: 0.8600 (m-30) REVERT: D 1168 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.6837 (t80) REVERT: D 1170 GLN cc_start: 0.8595 (pp30) cc_final: 0.8378 (pp30) outliers start: 115 outliers final: 84 residues processed: 335 average time/residue: 0.1417 time to fit residues: 84.9645 Evaluate side-chains 313 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 217 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 HIS Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 HIS Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [77, 103, 78, 56, 354, 306, 249, 184, 17, 338, 189] chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 chunk 306 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 338 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1153 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051507 restraints weight = 165173.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052941 restraints weight = 97581.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053890 restraints weight = 68787.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.054563 restraints weight = 54478.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054913 restraints weight = 46440.034| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30396 Z= 0.123 Angle : 0.675 13.783 41244 Z= 0.314 Chirality : 0.038 0.296 4660 Planarity : 0.005 0.053 5152 Dihedral : 6.903 57.182 4944 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.77 % Allowed : 26.70 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.15), residues: 3640 helix: 1.87 (0.11), residues: 2456 sheet: -2.70 (0.40), residues: 140 loop : -2.58 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 892 TYR 0.009 0.001 TYR D 256 PHE 0.025 0.001 PHE A 414 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS B1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30392) covalent geometry : angle 0.67476 / 0.31 (41236) SS BOND : bond 0.00113 / 0.05 ( 4) SS BOND : angle 0.18468 / 0.10 ( 8) hydrogen bonds : bond 0.03073 / 2.10 ( 1724) hydrogen bonds : angle 3.98932 / 2.87 ( 5148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 215 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8121 (mmm) cc_final: 0.7715 (mmm) REVERT: A 284 MET cc_start: 0.8192 (mmt) cc_final: 0.7571 (ptm) REVERT: A 410 GLN cc_start: 0.9591 (tp-100) cc_final: 0.9292 (tp-100) REVERT: A 562 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9332 (tp) REVERT: A 580 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8682 (mp0) REVERT: A 622 MET cc_start: 0.8789 (ttp) cc_final: 0.8516 (tmm) REVERT: A 641 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9306 (tt) REVERT: A 1153 GLN cc_start: 0.8943 (pp30) cc_final: 0.8659 (pp30) REVERT: A 1156 ASP cc_start: 0.9130 (m-30) cc_final: 0.8758 (m-30) REVERT: A 1170 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8873 (pp30) REVERT: B 186 MET cc_start: 0.8511 (mmm) cc_final: 0.7937 (mmm) REVERT: B 284 MET cc_start: 0.8071 (mmt) cc_final: 0.7501 (ptm) REVERT: B 410 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9291 (tp-100) REVERT: B 414 PHE cc_start: 0.8511 (t80) cc_final: 0.8292 (t80) REVERT: B 562 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9383 (tp) REVERT: B 580 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8673 (mt-10) REVERT: B 641 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9316 (tt) REVERT: B 684 MET cc_start: 0.8126 (tpp) cc_final: 0.7887 (tpp) REVERT: C 186 MET cc_start: 0.8214 (mmm) cc_final: 0.7964 (mmm) REVERT: C 225 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7640 (mm) REVERT: C 284 MET cc_start: 0.8119 (mmt) cc_final: 0.7559 (ptm) REVERT: C 410 GLN cc_start: 0.9581 (tp-100) cc_final: 0.9292 (tp-100) REVERT: C 414 PHE cc_start: 0.8497 (t80) cc_final: 0.8294 (t80) REVERT: C 562 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9390 (tp) REVERT: C 576 MET cc_start: 0.9334 (tpp) cc_final: 0.9001 (mmp) REVERT: C 580 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8682 (mp0) REVERT: C 622 MET cc_start: 0.8802 (ttp) cc_final: 0.8500 (tmm) REVERT: C 641 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9303 (tt) REVERT: C 1156 ASP cc_start: 0.8916 (m-30) cc_final: 0.8562 (m-30) REVERT: D 186 MET cc_start: 0.8518 (mmm) cc_final: 0.7985 (mmm) REVERT: D 284 MET cc_start: 0.8174 (mmt) cc_final: 0.7547 (ptm) REVERT: D 410 GLN cc_start: 0.9559 (tp-100) cc_final: 0.9338 (tp-100) REVERT: D 414 PHE cc_start: 0.8507 (t80) cc_final: 0.8218 (t80) REVERT: D 562 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9351 (tp) REVERT: D 580 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8657 (mt-10) REVERT: D 641 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9308 (tt) REVERT: D 1156 ASP cc_start: 0.9000 (m-30) cc_final: 0.8622 (m-30) REVERT: D 1168 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7394 (t80) REVERT: D 1170 GLN cc_start: 0.8600 (pp30) cc_final: 0.8387 (pp30) outliers start: 115 outliers final: 94 residues processed: 317 average time/residue: 0.1432 time to fit residues: 80.6036 Evaluate side-chains 318 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 214 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 HIS Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LEU Chi-restraints excluded: chain D residue 923 VAL Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: [209, 263, 72, 264, 75, 235, 84, 37, 336, 271, 60] chunk 209 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 264 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 235 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 37 optimal weight: 0.0980 chunk 336 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1153 GLN ** 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 = 0.3543 r_free = 0.3543 target = 0.067030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052092 restraints weight = 165572.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053541 restraints weight = 97309.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054510 restraints weight = 68287.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.055116 restraints weight = 54156.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.055567 restraints weight = 46689.390| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30396 Z= 0.112 Angle : 0.672 12.540 41244 Z= 0.311 Chirality : 0.038 0.299 4660 Planarity : 0.005 0.053 5152 Dihedral : 6.735 56.549 4944 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.47 % Allowed : 27.29 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.70 (0.15), residues: 3640 helix: 1.84 (0.11), residues: 2456 sheet: -2.66 (0.40), residues: 140 loop : -2.59 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 437 TYR 0.009 0.001 TYR D 256 PHE 0.022 0.001 PHE C 414 TRP 0.016 0.001 TRP A 152 HIS 0.002 0.001 HIS D1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (30392) covalent geometry : angle 0.67196 / 0.31 (41236) SS BOND : bond 0.00078 / 0.04 ( 4) SS BOND : angle 0.24191 / 0.13 ( 8) hydrogen bonds : bond 0.03031 / 2.07 ( 1724) hydrogen bonds : angle 3.97211 / 2.86 ( 5148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.79 seconds wall clock time: 79 minutes 53.33 seconds (4793.33 seconds total)