Starting phenix.real_space_refine on Sun Jul 5 21:30:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9smk_55036/07_2026/9smk_55036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9smk_55036/07_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_55036/07_2026/9smk_55036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9smk_55036/07_2026/9smk_55036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9smk_55036/07_2026/9smk_55036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9smk_55036/07_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-dev-6108/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, 105 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 105 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Restraints were copied for chains: B, D Time building chain proxies: 15.87, 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=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 298 " distance=0.00 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 310 " distance=0.00 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 385 " distance=0.00 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 593 " distance=0.00 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 630 " distance=0.00 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 646 " distance=0.00 Simple disulfide: pdb=" SG CYS B 654 " - pdb=" SG CYS B 654 " distance=0.00 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 699 " distance=0.00 Simple disulfide: pdb=" SG CYS B 768 " - pdb=" SG CYS B 768 " distance=0.00 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 826 " distance=0.00 Simple disulfide: pdb=" SG CYS B 867 " - pdb=" SG CYS B 867 " distance=0.00 Simple disulfide: pdb=" SG CYS B 874 " - pdb=" SG CYS B 874 " distance=0.00 Simple disulfide: pdb=" SG CYS B 881 " - pdb=" SG CYS B 881 " distance=0.00 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 896 " distance=0.00 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B 993 " distance=0.00 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B1011 " - pdb=" SG CYS B 993 " distance=2.03 Simple disulfide: pdb=" SG CYS B1011 " - pdb=" SG CYS B1011 " distance=0.00 Simple disulfide: pdb=" SG CYS B1093 " - pdb=" SG CYS B1093 " distance=0.00 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " 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: 2.69 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: 0.64 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: 5.63 Time building geometry restraints manager: 3.57 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: 16161 17.57 - 35.14: 1726 35.14 - 52.70: 573 52.70 - 70.27: 76 70.27 - 87.84: 44 Dihedral angle restraints: 18580 sinusoidal: 7904 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 18577 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: 2.03 - 2.60: 222 2.60 - 3.18: 25772 3.18 - 3.75: 48062 3.75 - 4.33: 60712 4.33 - 4.90: 99988 Nonbonded interactions: 234756 Sorted by model distance: nonbonded pdb=" SG CYS D 993 " pdb=" SG CYS D1011 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 993 " pdb=" SG CYS C1011 " model vdw 2.028 3.760 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 ... (remaining 234751 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: 8.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.980 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- 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 30394 Z= 0.152 Angle : 0.639 9.394 41257 Z= 0.317 Chirality : 0.038 0.185 4660 Planarity : 0.005 0.064 5152 Dihedral : 16.407 87.838 11644 Min Nonbonded Distance : 2.028 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 0.00253 / 0.13 ( 2) SS BOND : angle 0.08891 / 0.06 ( 21) 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 : 1.099 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: 0.7463 (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: 0.5950 (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: 0.7892 (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: 0.7449 (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: 0.6159 (t80) REVERT: D 622 MET cc_start: 0.5739 (ttp) cc_final: 0.5151 (ttm) REVERT: D 641 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7486 (tt) REVERT: D 817 LEU cc_start: 0.8281 (tp) cc_final: 0.8018 (tt) outliers start: 65 outliers final: 20 residues processed: 501 average time/residue: 0.2069 time to fit residues: 159.8978 Evaluate side-chains 282 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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: 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 410 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 ** B1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN C 424 HIS ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 HIS C1014 GLN C1032 ASN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D1032 ASN ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.067523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051826 restraints weight = 164946.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053210 restraints weight = 101182.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054112 restraints weight = 73282.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054764 restraints weight = 59118.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.055030 restraints weight = 50919.622| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30394 Z= 0.344 Angle : 0.770 8.965 41257 Z= 0.390 Chirality : 0.042 0.173 4660 Planarity : 0.006 0.055 5152 Dihedral : 7.964 57.110 4976 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 8.55 % Allowed : 20.74 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.14), residues: 3640 helix: 1.39 (0.11), residues: 2452 sheet: -3.64 (0.31), residues: 192 loop : -2.61 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 334 TYR 0.015 0.002 TYR B 229 PHE 0.026 0.002 PHE C 627 TRP 0.013 0.002 TRP C 776 HIS 0.004 0.001 HIS B1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.34 (30392) covalent geometry : angle 0.77055 / 0.39 (41236) SS BOND : bond 0.00321 / 0.16 ( 2) SS BOND : angle 0.14074 / 0.10 ( 21) hydrogen bonds : bond 0.04002 / 2.71 ( 1724) hydrogen bonds : angle 4.39704 / 3.15 ( 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 504 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 243 time to evaluate : 1.107 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: 0.9140 (OUTLIER) cc_final: 0.8912 (mt) REVERT: A 414 PHE cc_start: 0.8741 (t80) cc_final: 0.8507 (t80) REVERT: A 562 LEU cc_start: 0.9793 (OUTLIER) cc_final: 0.9561 (tp) REVERT: A 641 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9410 (tt) REVERT: A 817 LEU cc_start: 0.9775 (tp) cc_final: 0.9451 (tt) REVERT: A 1154 LYS cc_start: 0.9672 (OUTLIER) cc_final: 0.8877 (ptmm) REVERT: A 1156 ASP cc_start: 0.9224 (m-30) cc_final: 0.8871 (m-30) REVERT: A 1168 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.6543 (t80) REVERT: B 449 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8144 (mm) REVERT: B 562 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9533 (tp) REVERT: B 574 MET cc_start: 0.9118 (tpp) cc_final: 0.8823 (mpp) REVERT: B 641 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9422 (tt) REVERT: B 708 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.7667 (tt) REVERT: B 817 LEU cc_start: 0.9769 (tp) cc_final: 0.9441 (tt) REVERT: B 1146 GLU cc_start: 0.9463 (tp30) cc_final: 0.8847 (tp30) REVERT: B 1154 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9192 (ttpp) REVERT: B 1168 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.6760 (t80) REVERT: C 449 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8155 (mm) REVERT: C 562 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9548 (tp) REVERT: C 641 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9420 (tt) REVERT: C 792 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9564 (mm) REVERT: C 817 LEU cc_start: 0.9775 (tp) cc_final: 0.9453 (tt) REVERT: C 1146 GLU cc_start: 0.9443 (tp30) cc_final: 0.8836 (tp30) REVERT: C 1154 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9195 (ptmm) REVERT: C 1168 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.6460 (t80) REVERT: D 376 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8876 (mt) REVERT: D 449 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8221 (mm) REVERT: D 562 LEU cc_start: 0.9795 (OUTLIER) cc_final: 0.9563 (tp) REVERT: D 641 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9411 (tt) REVERT: D 792 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9557 (mm) REVERT: D 817 LEU cc_start: 0.9779 (tp) cc_final: 0.9456 (tt) REVERT: D 1154 LYS cc_start: 0.9671 (OUTLIER) cc_final: 0.9307 (ptmm) REVERT: D 1156 ASP cc_start: 0.9227 (m-30) cc_final: 0.8950 (m-30) REVERT: D 1168 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.6411 (t80) outliers start: 261 outliers final: 112 residues processed: 467 average time/residue: 0.1649 time to fit residues: 129.8694 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 : 1.077 ------------------------------------------------------------------------------- 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 443 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 703 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 300 LEU 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 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 622 MET 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 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 443 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 703 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 1023 LEU Chi-restraints excluded: chain D residue 1040 ILE 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: chunk 335 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 272 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 303 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** A1061 GLN 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** B1061 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 ASN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN D 174 GLN D 410 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1032 ASN ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.068908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053722 restraints weight = 165121.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055191 restraints weight = 98089.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056147 restraints weight = 69562.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056804 restraints weight = 55352.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057209 restraints weight = 47290.095| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30394 Z= 0.168 Angle : 0.647 10.150 41257 Z= 0.315 Chirality : 0.038 0.154 4660 Planarity : 0.005 0.054 5152 Dihedral : 7.575 58.743 4950 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.67 % Allowed : 23.92 % Favored : 70.41 % 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: 0.34 (0.14), residues: 3640 helix: 1.60 (0.11), residues: 2448 sheet: -3.22 (0.36), residues: 148 loop : -2.68 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 405 TYR 0.012 0.001 TYR C1063 PHE 0.016 0.001 PHE C 627 TRP 0.014 0.002 TRP C1000 HIS 0.003 0.001 HIS D1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (30392) covalent geometry : angle 0.64723 / 0.32 (41236) SS BOND : bond 0.00071 / 0.04 ( 2) SS BOND : angle 0.02264 / 0.01 ( 21) hydrogen bonds : bond 0.03544 / 2.40 ( 1724) hydrogen bonds : angle 4.15128 / 2.97 ( 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 415 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 242 time to evaluate : 1.098 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: A 376 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8948 (mt) REVERT: A 414 PHE cc_start: 0.8598 (t80) cc_final: 0.8322 (t80) REVERT: A 562 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9533 (tp) REVERT: A 641 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9419 (tt) REVERT: A 784 MET cc_start: 0.9102 (tpt) cc_final: 0.8857 (tpt) REVERT: A 900 MET cc_start: 0.9367 (mmm) cc_final: 0.9074 (tpt) REVERT: A 1154 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9146 (ptmm) REVERT: A 1168 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 1170 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8784 (pp30) REVERT: B 562 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9521 (tp) REVERT: B 641 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9422 (tt) REVERT: B 784 MET cc_start: 0.9102 (tpt) cc_final: 0.8856 (tpt) REVERT: B 1146 GLU cc_start: 0.9435 (tp30) cc_final: 0.8843 (tp30) REVERT: B 1154 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9216 (ptmm) REVERT: B 1168 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.6762 (t80) REVERT: C 376 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8938 (mt) REVERT: C 562 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9526 (tp) REVERT: C 641 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9421 (tt) REVERT: C 784 MET cc_start: 0.9100 (tpt) cc_final: 0.8860 (tpt) REVERT: C 792 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9565 (mm) REVERT: C 1146 GLU cc_start: 0.9422 (tp30) cc_final: 0.8833 (tp30) REVERT: C 1154 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9163 (ptmm) REVERT: C 1168 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6579 (t80) REVERT: D 376 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8940 (mt) REVERT: D 562 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9537 (tp) REVERT: D 641 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9426 (tt) REVERT: D 784 MET cc_start: 0.9095 (tpt) cc_final: 0.8847 (tpt) REVERT: D 792 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9549 (mm) REVERT: D 1168 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.6657 (t80) outliers start: 173 outliers final: 95 residues processed: 383 average time/residue: 0.1688 time to fit residues: 108.8332 Evaluate side-chains 340 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 225 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 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 1023 LEU Chi-restraints excluded: chain A residue 1040 ILE 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 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 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 709 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 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 1154 LYS Chi-restraints excluded: chain B residue 1168 TYR 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 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 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 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 923 VAL Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1040 ILE 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 792 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 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: chunk 263 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 365 optimal weight: 0.0370 chunk 113 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 669 GLN ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 410 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 410 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1037 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.067411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052431 restraints weight = 167099.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053823 restraints weight = 99075.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054765 restraints weight = 70396.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055398 restraints weight = 55846.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055774 restraints weight = 47716.541| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30394 Z= 0.189 Angle : 0.640 8.861 41257 Z= 0.316 Chirality : 0.038 0.154 4660 Planarity : 0.005 0.054 5152 Dihedral : 7.385 59.370 4950 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 6.29 % Allowed : 22.97 % Favored : 70.74 % 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: 0.47 (0.14), residues: 3640 helix: 1.67 (0.11), residues: 2460 sheet: -3.68 (0.38), residues: 108 loop : -2.61 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 612 TYR 0.013 0.001 TYR D 971 PHE 0.018 0.001 PHE C 627 TRP 0.015 0.002 TRP D 152 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (30392) covalent geometry : angle 0.64000 / 0.32 (41236) SS BOND : bond 0.00106 / 0.05 ( 2) SS BOND : angle 0.01726 / 0.01 ( 21) hydrogen bonds : bond 0.03433 / 2.32 ( 1724) hydrogen bonds : angle 4.13117 / 2.96 ( 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 421 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 229 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8883 (mtt) cc_final: 0.8635 (mtt) REVERT: A 284 MET cc_start: 0.8047 (mmt) cc_final: 0.7534 (mmp) REVERT: A 313 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: A 410 GLN cc_start: 0.9628 (tp-100) cc_final: 0.9346 (tp-100) REVERT: A 562 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9531 (tp) REVERT: A 641 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9401 (tt) REVERT: A 784 MET cc_start: 0.9124 (tpt) cc_final: 0.8838 (tpt) REVERT: A 900 MET cc_start: 0.9380 (mmm) cc_final: 0.9058 (tpt) REVERT: A 1168 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 1170 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8824 (pp30) REVERT: B 175 MET cc_start: 0.8843 (mtt) cc_final: 0.8623 (mtt) REVERT: B 184 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 186 MET cc_start: 0.8589 (mmm) cc_final: 0.8102 (mmt) REVERT: B 313 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8678 (pt0) REVERT: B 394 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8851 (mt) REVERT: B 562 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9526 (tp) REVERT: B 641 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9387 (tt) REVERT: B 675 LEU cc_start: 0.9601 (tp) cc_final: 0.9383 (tt) REVERT: B 784 MET cc_start: 0.9118 (tpt) cc_final: 0.8833 (tpt) REVERT: B 900 MET cc_start: 0.9482 (mmm) cc_final: 0.9273 (mmm) REVERT: B 1038 LEU cc_start: 0.9790 (tt) cc_final: 0.9580 (tp) REVERT: B 1146 GLU cc_start: 0.9445 (tp30) cc_final: 0.8822 (tp30) REVERT: B 1168 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.6915 (t80) REVERT: C 186 MET cc_start: 0.8414 (mmm) cc_final: 0.7951 (mmp) REVERT: C 313 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: C 414 PHE cc_start: 0.8582 (t80) cc_final: 0.8382 (t80) REVERT: C 562 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9527 (tp) REVERT: C 622 MET cc_start: 0.8825 (ttp) cc_final: 0.8368 (tmm) REVERT: C 641 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9400 (tt) REVERT: C 675 LEU cc_start: 0.9602 (tp) cc_final: 0.9392 (tt) REVERT: C 784 MET cc_start: 0.9112 (tpt) cc_final: 0.8836 (tpt) REVERT: C 1146 GLU cc_start: 0.9431 (tp30) cc_final: 0.8805 (tp30) REVERT: C 1168 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.6743 (t80) REVERT: D 175 MET cc_start: 0.8865 (mtt) cc_final: 0.8610 (mtt) REVERT: D 186 MET cc_start: 0.8483 (mmm) cc_final: 0.8035 (mmp) REVERT: D 313 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8697 (pt0) REVERT: D 410 GLN cc_start: 0.9624 (tp-100) cc_final: 0.9341 (tp-100) REVERT: D 414 PHE cc_start: 0.8558 (t80) cc_final: 0.8282 (t80) REVERT: D 562 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9535 (tp) REVERT: D 613 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9308 (mmtm) REVERT: D 641 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9392 (tt) REVERT: D 675 LEU cc_start: 0.9609 (tp) cc_final: 0.9407 (tt) REVERT: D 784 MET cc_start: 0.9107 (tpt) cc_final: 0.8824 (tpt) REVERT: D 900 MET cc_start: 0.9481 (mmm) cc_final: 0.9273 (mmm) REVERT: D 1154 LYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9267 (ptmm) REVERT: D 1168 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.6725 (t80) outliers start: 192 outliers final: 108 residues processed: 393 average time/residue: 0.1556 time to fit residues: 105.3494 Evaluate side-chains 339 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 211 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 399 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 669 GLN 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 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 1148 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 117 LEU Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 184 VAL 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 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 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 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 1168 TYR Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 138 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 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 510 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 781 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 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 1023 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1148 LEU 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 138 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 313 GLU 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 613 LYS 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 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 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 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: chunk 56 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 348 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 146 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN B 410 GLN ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 410 GLN ** D1153 GLN ** 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 = 0.3558 r_free = 0.3558 target = 0.068933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054031 restraints weight = 164281.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055495 restraints weight = 96753.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056470 restraints weight = 68368.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057135 restraints weight = 54176.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057581 restraints weight = 46405.104| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30394 Z= 0.114 Angle : 0.625 9.472 41257 Z= 0.300 Chirality : 0.037 0.161 4660 Planarity : 0.005 0.053 5152 Dihedral : 7.322 59.930 4950 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.65 % Allowed : 24.41 % Favored : 70.94 % 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: 0.55 (0.15), residues: 3640 helix: 1.75 (0.11), residues: 2460 sheet: -2.96 (0.38), residues: 148 loop : -2.66 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1150 TYR 0.008 0.001 TYR B 256 PHE 0.023 0.001 PHE A 414 TRP 0.015 0.001 TRP A 152 HIS 0.002 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (30392) covalent geometry : angle 0.62494 / 0.30 (41236) SS BOND : bond 0.00010 / 0.00 ( 2) SS BOND : angle 0.08827 / 0.06 ( 21) hydrogen bonds : bond 0.03206 / 2.18 ( 1724) hydrogen bonds : angle 3.99600 / 2.89 ( 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 385 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 243 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8398 (mmm) cc_final: 0.7838 (mmp) REVERT: A 284 MET cc_start: 0.7997 (mmt) cc_final: 0.7473 (mmp) REVERT: A 410 GLN cc_start: 0.9620 (tp-100) cc_final: 0.9270 (tp-100) REVERT: A 414 PHE cc_start: 0.8591 (t80) cc_final: 0.8261 (t80) REVERT: A 562 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9506 (tp) REVERT: A 641 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9362 (tt) REVERT: A 684 MET cc_start: 0.8373 (mmt) cc_final: 0.8057 (tpp) REVERT: A 900 MET cc_start: 0.9355 (mmm) cc_final: 0.9008 (tpt) REVERT: A 1154 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9194 (ptmm) REVERT: A 1168 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 1170 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8829 (pp30) REVERT: B 175 MET cc_start: 0.8798 (mtt) cc_final: 0.8570 (mtt) REVERT: B 184 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 394 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8833 (mt) REVERT: B 562 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9510 (tp) REVERT: B 576 MET cc_start: 0.9271 (mmp) cc_final: 0.8968 (mmp) REVERT: B 580 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8518 (mp0) REVERT: B 641 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9353 (tt) REVERT: B 675 LEU cc_start: 0.9601 (tp) cc_final: 0.9393 (tt) REVERT: B 1146 GLU cc_start: 0.9429 (tp30) cc_final: 0.8817 (tp30) REVERT: B 1153 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8983 (pp30) REVERT: B 1168 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.6783 (t80) REVERT: C 186 MET cc_start: 0.8403 (mmm) cc_final: 0.7977 (mmp) REVERT: C 225 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (mm) REVERT: C 284 MET cc_start: 0.7902 (mmt) cc_final: 0.7375 (mmp) REVERT: C 562 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9509 (tp) REVERT: C 641 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9369 (tt) REVERT: C 675 LEU cc_start: 0.9600 (tp) cc_final: 0.9395 (tt) REVERT: C 900 MET cc_start: 0.9526 (mmm) cc_final: 0.9312 (mmm) REVERT: C 1146 GLU cc_start: 0.9424 (tp30) cc_final: 0.8808 (tp30) REVERT: C 1156 ASP cc_start: 0.9143 (m-30) cc_final: 0.8817 (m-30) REVERT: D 175 MET cc_start: 0.8863 (mtt) cc_final: 0.8634 (mtt) REVERT: D 186 MET cc_start: 0.8480 (mmm) cc_final: 0.8055 (mmp) REVERT: D 284 MET cc_start: 0.7960 (mmt) cc_final: 0.7441 (mmp) REVERT: D 410 GLN cc_start: 0.9604 (tp-100) cc_final: 0.9298 (tp-100) REVERT: D 414 PHE cc_start: 0.8565 (t80) cc_final: 0.8293 (t80) REVERT: D 562 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9514 (tp) REVERT: D 641 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9355 (tt) REVERT: D 675 LEU cc_start: 0.9611 (tp) cc_final: 0.9407 (tt) REVERT: D 684 MET cc_start: 0.8342 (mmt) cc_final: 0.8069 (tpp) REVERT: D 1156 ASP cc_start: 0.8765 (m-30) cc_final: 0.8540 (m-30) REVERT: D 1168 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7216 (t80) outliers start: 142 outliers final: 86 residues processed: 366 average time/residue: 0.1641 time to fit residues: 103.9813 Evaluate side-chains 321 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 220 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 1002 HIS Chi-restraints excluded: chain A residue 1087 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 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 184 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 300 LEU 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 1148 LEU 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 117 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 173 HIS 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 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 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 923 VAL Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain D residue 90 PHE 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 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 1040 ILE Chi-restraints excluded: chain D residue 1087 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: chunk 296 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 354 optimal weight: 0.4980 chunk 6 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1037 ASN ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** D1037 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 = 0.3505 r_free = 0.3505 target = 0.065793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050540 restraints weight = 167034.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.051949 restraints weight = 98697.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052878 restraints weight = 69877.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053512 restraints weight = 55716.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053961 restraints weight = 47760.937| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30394 Z= 0.188 Angle : 0.652 9.390 41257 Z= 0.320 Chirality : 0.038 0.144 4660 Planarity : 0.005 0.054 5152 Dihedral : 7.300 59.814 4950 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.44 % Allowed : 23.95 % Favored : 70.61 % 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: 0.65 (0.15), residues: 3640 helix: 1.80 (0.11), residues: 2464 sheet: -2.97 (0.37), residues: 148 loop : -2.55 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 612 TYR 0.011 0.001 TYR B1063 PHE 0.022 0.001 PHE A 414 TRP 0.017 0.002 TRP A 152 HIS 0.003 0.001 HIS B1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (30392) covalent geometry : angle 0.65169 / 0.32 (41236) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 0.01388 / 0.01 ( 21) hydrogen bonds : bond 0.03445 / 2.33 ( 1724) hydrogen bonds : angle 4.07239 / 2.94 ( 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 389 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 223 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7821 (mm) REVERT: A 284 MET cc_start: 0.8133 (mmt) cc_final: 0.7737 (mmp) REVERT: A 410 GLN cc_start: 0.9625 (tp-100) cc_final: 0.9341 (tp-100) REVERT: A 562 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9533 (tp) REVERT: A 641 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9362 (tt) REVERT: A 900 MET cc_start: 0.9380 (mmm) cc_final: 0.9039 (tpt) REVERT: A 1154 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9175 (ptmm) REVERT: A 1156 ASP cc_start: 0.9120 (m-30) cc_final: 0.8750 (m-30) REVERT: A 1168 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.6824 (t80) REVERT: A 1170 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8862 (pp30) REVERT: B 184 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.7960 (p) REVERT: B 186 MET cc_start: 0.8632 (mmm) cc_final: 0.8015 (mmm) REVERT: B 313 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8718 (pt0) REVERT: B 410 GLN cc_start: 0.9618 (tp-100) cc_final: 0.9353 (tp-100) REVERT: B 414 PHE cc_start: 0.8651 (t80) cc_final: 0.8351 (t80) REVERT: B 562 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9533 (tp) REVERT: B 580 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8743 (mt-10) REVERT: B 641 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9362 (tt) REVERT: B 1146 GLU cc_start: 0.9441 (tp30) cc_final: 0.8814 (tp30) REVERT: B 1168 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.6868 (t80) REVERT: C 186 MET cc_start: 0.8405 (mmm) cc_final: 0.8167 (mmm) REVERT: C 225 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7655 (mm) REVERT: C 313 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8741 (pt0) REVERT: C 414 PHE cc_start: 0.8586 (t80) cc_final: 0.8304 (t80) REVERT: C 562 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9524 (tp) REVERT: C 580 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8724 (mt-10) REVERT: C 641 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9375 (tt) REVERT: C 1146 GLU cc_start: 0.9433 (tp30) cc_final: 0.8800 (tp30) REVERT: C 1156 ASP cc_start: 0.9136 (m-30) cc_final: 0.8836 (m-30) REVERT: C 1168 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.6812 (t80) REVERT: D 284 MET cc_start: 0.8111 (mmt) cc_final: 0.7718 (mmp) REVERT: D 410 GLN cc_start: 0.9613 (tp-100) cc_final: 0.9332 (tp-100) REVERT: D 562 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9527 (tp) REVERT: D 613 LYS cc_start: 0.9530 (OUTLIER) cc_final: 0.9273 (mmtm) REVERT: D 641 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9359 (tt) REVERT: D 684 MET cc_start: 0.8372 (mmt) cc_final: 0.8131 (tpp) REVERT: D 1154 LYS cc_start: 0.9611 (OUTLIER) cc_final: 0.9232 (ttpp) REVERT: D 1168 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.6996 (t80) outliers start: 166 outliers final: 99 residues processed: 365 average time/residue: 0.1544 time to fit residues: 97.2595 Evaluate side-chains 332 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 213 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 225 LEU 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 690 ILE 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 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1088 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 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 184 VAL 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 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 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 1087 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 117 LEU Chi-restraints excluded: chain C residue 138 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 313 GLU 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 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 1088 LEU Chi-restraints excluded: chain C residue 1148 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 613 LYS 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 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 1154 LYS 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: chunk 271 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 GLN B1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051824 restraints weight = 168343.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053253 restraints weight = 98165.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054188 restraints weight = 69033.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054850 restraints weight = 54519.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055087 restraints weight = 46432.923| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30394 Z= 0.161 Angle : 0.658 12.218 41257 Z= 0.316 Chirality : 0.038 0.154 4660 Planarity : 0.005 0.053 5152 Dihedral : 7.261 59.931 4950 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.82 % Allowed : 25.13 % Favored : 70.05 % 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: 2468 sheet: -2.84 (0.38), residues: 148 loop : -2.56 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 437 TYR 0.009 0.001 TYR B 256 PHE 0.022 0.001 PHE D 414 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS B1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (30392) covalent geometry : angle 0.65810 / 0.32 (41236) SS BOND : bond 0.00084 / 0.04 ( 2) SS BOND : angle 0.04657 / 0.03 ( 21) hydrogen bonds : bond 0.03232 / 2.19 ( 1724) hydrogen bonds : angle 4.06053 / 2.93 ( 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 366 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 219 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8171 (mmm) cc_final: 0.7966 (mmm) REVERT: A 284 MET cc_start: 0.8129 (mmt) cc_final: 0.7744 (mmp) REVERT: A 410 GLN cc_start: 0.9612 (tp-100) cc_final: 0.9340 (tp-100) REVERT: A 562 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9528 (tp) REVERT: A 641 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9358 (tt) REVERT: A 900 MET cc_start: 0.9366 (mmm) cc_final: 0.9033 (tpt) REVERT: A 1154 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.8999 (ptmm) REVERT: A 1156 ASP cc_start: 0.9099 (m-30) cc_final: 0.8730 (m-30) REVERT: A 1168 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7160 (t80) REVERT: A 1170 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8919 (pp30) REVERT: B 284 MET cc_start: 0.8030 (mmt) cc_final: 0.7613 (mmp) REVERT: B 410 GLN cc_start: 0.9594 (tp40) cc_final: 0.9309 (tp-100) REVERT: B 414 PHE cc_start: 0.8551 (t80) cc_final: 0.8343 (t80) REVERT: B 562 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9398 (tp) REVERT: B 580 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8689 (mt-10) REVERT: B 641 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9363 (tt) REVERT: B 1146 GLU cc_start: 0.9413 (tp30) cc_final: 0.8793 (tp30) REVERT: C 225 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7708 (mm) REVERT: C 284 MET cc_start: 0.8071 (mmt) cc_final: 0.7667 (mmp) REVERT: C 562 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9539 (tp) REVERT: C 580 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8678 (mt-10) REVERT: C 641 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9354 (tt) REVERT: C 684 MET cc_start: 0.8312 (mmt) cc_final: 0.7999 (tpp) REVERT: C 1146 GLU cc_start: 0.9395 (tp30) cc_final: 0.8770 (tp30) REVERT: C 1156 ASP cc_start: 0.9118 (m-30) cc_final: 0.8796 (m-30) REVERT: C 1168 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.6931 (t80) REVERT: D 186 MET cc_start: 0.8509 (mmm) cc_final: 0.8032 (mmm) REVERT: D 284 MET cc_start: 0.8125 (mmt) cc_final: 0.7739 (mmp) REVERT: D 410 GLN cc_start: 0.9602 (tp-100) cc_final: 0.9337 (tp-100) REVERT: D 562 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9528 (tp) REVERT: D 580 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8701 (mt-10) REVERT: D 641 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9357 (tt) REVERT: D 1168 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7121 (t80) outliers start: 147 outliers final: 100 residues processed: 352 average time/residue: 0.1603 time to fit residues: 97.6360 Evaluate side-chains 319 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 206 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR 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 792 LEU 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 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 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 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 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 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 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 1040 ILE Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 138 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 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 510 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 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 1025 VAL Chi-restraints excluded: chain C residue 1148 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 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 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 792 LEU Chi-restraints excluded: chain D residue 824 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 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 1025 VAL Chi-restraints excluded: chain D residue 1148 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: chunk 40 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 34 optimal weight: 0.2980 chunk 114 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050835 restraints weight = 165180.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052243 restraints weight = 97552.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053221 restraints weight = 68749.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053882 restraints weight = 54082.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054232 restraints weight = 46095.662| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30394 Z= 0.145 Angle : 0.661 11.057 41257 Z= 0.316 Chirality : 0.038 0.181 4660 Planarity : 0.005 0.053 5152 Dihedral : 7.231 59.934 4950 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.52 % Allowed : 25.82 % Favored : 69.66 % 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: 2464 sheet: -2.79 (0.38), residues: 148 loop : -2.56 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 953 TYR 0.010 0.001 TYR D 256 PHE 0.025 0.001 PHE A 414 TRP 0.018 0.001 TRP C 579 HIS 0.003 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (30392) covalent geometry : angle 0.66153 / 0.32 (41236) SS BOND : bond 0.00164 / 0.08 ( 2) SS BOND : angle 0.01085 / 0.01 ( 21) hydrogen bonds : bond 0.03221 / 2.19 ( 1724) hydrogen bonds : angle 4.03612 / 2.91 ( 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 353 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 215 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8238 (mmm) cc_final: 0.7656 (mmt) REVERT: A 225 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 284 MET cc_start: 0.8172 (mmt) cc_final: 0.7787 (mmp) REVERT: A 410 GLN cc_start: 0.9599 (tp-100) cc_final: 0.9347 (tp-100) REVERT: A 449 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 562 LEU cc_start: 0.9760 (OUTLIER) cc_final: 0.9517 (tp) REVERT: A 641 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9349 (tt) REVERT: A 900 MET cc_start: 0.9359 (mmm) cc_final: 0.9038 (tpt) REVERT: A 1154 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8962 (ptmm) REVERT: A 1156 ASP cc_start: 0.9069 (m-30) cc_final: 0.8690 (m-30) REVERT: A 1168 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.6731 (t80) REVERT: A 1170 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8834 (pp30) REVERT: B 186 MET cc_start: 0.8558 (mmm) cc_final: 0.7828 (mmp) REVERT: B 284 MET cc_start: 0.8076 (mmt) cc_final: 0.7633 (mmp) REVERT: B 410 GLN cc_start: 0.9600 (tp40) cc_final: 0.9316 (tp-100) REVERT: B 562 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9513 (tp) REVERT: B 580 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8689 (mt-10) REVERT: B 641 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9352 (tt) REVERT: B 1146 GLU cc_start: 0.9391 (tp30) cc_final: 0.8783 (tp30) REVERT: B 1168 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6646 (t80) REVERT: C 186 MET cc_start: 0.8112 (mmm) cc_final: 0.7609 (mmm) REVERT: C 225 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7695 (mm) REVERT: C 284 MET cc_start: 0.8114 (mmt) cc_final: 0.7698 (mmp) REVERT: C 414 PHE cc_start: 0.8586 (t80) cc_final: 0.8382 (t80) REVERT: C 562 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9524 (tp) REVERT: C 580 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8689 (mt-10) REVERT: C 641 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9349 (tt) REVERT: C 684 MET cc_start: 0.8218 (mmt) cc_final: 0.7942 (tpp) REVERT: C 1146 GLU cc_start: 0.9392 (tp30) cc_final: 0.8776 (tp30) REVERT: C 1156 ASP cc_start: 0.9106 (m-30) cc_final: 0.8774 (m-30) REVERT: C 1168 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.6897 (t80) REVERT: D 284 MET cc_start: 0.8131 (mmt) cc_final: 0.7751 (mmp) REVERT: D 410 GLN cc_start: 0.9589 (tp-100) cc_final: 0.9339 (tp-100) REVERT: D 562 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9505 (tp) REVERT: D 580 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8695 (mt-10) REVERT: D 641 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9347 (tt) REVERT: D 1168 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.6914 (t80) outliers start: 138 outliers final: 100 residues processed: 338 average time/residue: 0.1621 time to fit residues: 96.0712 Evaluate side-chains 327 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 211 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 225 LEU 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 449 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 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 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 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 375 THR 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 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 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 1148 LEU Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 138 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 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 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 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 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 1025 VAL Chi-restraints excluded: chain C residue 1040 ILE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1148 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 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 824 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 934 LEU Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1025 VAL 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: chunk 67 optimal weight: 5.9990 chunk 302 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 187 optimal weight: 0.0070 chunk 77 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 331 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1170 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 = 0.3538 r_free = 0.3538 target = 0.066929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052137 restraints weight = 163247.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053552 restraints weight = 95983.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054518 restraints weight = 67477.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.055201 restraints weight = 53265.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.055599 restraints weight = 45188.315| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30394 Z= 0.114 Angle : 0.673 13.041 41257 Z= 0.313 Chirality : 0.038 0.269 4660 Planarity : 0.004 0.053 5152 Dihedral : 7.114 57.903 4946 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.54 % Allowed : 26.83 % Favored : 69.63 % 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: 0.74 (0.15), residues: 3640 helix: 1.87 (0.11), residues: 2464 sheet: -2.75 (0.38), residues: 148 loop : -2.57 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 437 TYR 0.009 0.001 TYR B 256 PHE 0.024 0.001 PHE D 414 TRP 0.016 0.001 TRP A 152 HIS 0.002 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (30392) covalent geometry : angle 0.67297 / 0.31 (41236) SS BOND : bond 0.00075 / 0.04 ( 2) SS BOND : angle 0.06188 / 0.04 ( 21) hydrogen bonds : bond 0.03077 / 2.10 ( 1724) hydrogen bonds : angle 3.96840 / 2.86 ( 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 345 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 237 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 186 MET cc_start: 0.8214 (mmm) cc_final: 0.7598 (mmt) REVERT: A 225 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7731 (mm) REVERT: A 284 MET cc_start: 0.8158 (mmt) cc_final: 0.7534 (ptm) REVERT: A 410 GLN cc_start: 0.9588 (tp-100) cc_final: 0.9331 (tp-100) REVERT: A 562 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9471 (tp) REVERT: A 580 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 641 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9317 (tt) REVERT: A 900 MET cc_start: 0.9335 (mmm) cc_final: 0.8999 (tpt) REVERT: A 1153 GLN cc_start: 0.9039 (pp30) cc_final: 0.8776 (pp30) REVERT: A 1156 ASP cc_start: 0.9074 (m-30) cc_final: 0.8693 (m-30) REVERT: A 1168 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 1170 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8863 (pp30) REVERT: B 186 MET cc_start: 0.8491 (mmm) cc_final: 0.8009 (mmm) REVERT: B 284 MET cc_start: 0.8042 (mmt) cc_final: 0.7608 (mmp) REVERT: B 414 PHE cc_start: 0.8462 (t80) cc_final: 0.8181 (t80) REVERT: B 562 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9480 (tp) REVERT: B 580 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8537 (mt-10) REVERT: B 641 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9308 (tt) REVERT: B 934 LEU cc_start: 0.9701 (tp) cc_final: 0.9472 (tt) REVERT: B 1146 GLU cc_start: 0.9372 (tp30) cc_final: 0.8773 (tp30) REVERT: B 1168 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.6640 (t80) REVERT: C 186 MET cc_start: 0.8126 (mmm) cc_final: 0.7637 (mmm) REVERT: C 225 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7666 (mm) REVERT: C 284 MET cc_start: 0.8071 (mmt) cc_final: 0.7642 (mmp) REVERT: C 562 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9491 (tp) REVERT: C 580 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 641 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9315 (tt) REVERT: C 936 PHE cc_start: 0.9196 (t80) cc_final: 0.8951 (t80) REVERT: C 1146 GLU cc_start: 0.9358 (tp30) cc_final: 0.8732 (tp30) REVERT: C 1156 ASP cc_start: 0.9088 (m-30) cc_final: 0.8775 (m-30) REVERT: D 186 MET cc_start: 0.8165 (mmm) cc_final: 0.7328 (mmp) REVERT: D 284 MET cc_start: 0.8135 (mmt) cc_final: 0.7519 (ptm) REVERT: D 410 GLN cc_start: 0.9577 (tp-100) cc_final: 0.9277 (tp-100) REVERT: D 562 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9327 (tp) REVERT: D 580 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8655 (mt-10) REVERT: D 641 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9307 (tt) REVERT: D 1154 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9259 (ptmm) REVERT: D 1168 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7174 (t80) outliers start: 108 outliers final: 82 residues processed: 339 average time/residue: 0.1576 time to fit residues: 94.1183 Evaluate side-chains 307 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 211 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR 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 225 LEU 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 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 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 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 375 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 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 789 SER 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 1088 LEU Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 138 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 433 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 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 1025 VAL Chi-restraints excluded: chain C residue 1040 ILE Chi-restraints excluded: chain C residue 1088 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 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 824 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 1025 VAL Chi-restraints excluded: chain D residue 1154 LYS 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: chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 354 optimal weight: 20.0000 chunk 306 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 GLN B1037 ASN C1037 ASN ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.066407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051688 restraints weight = 163637.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053073 restraints weight = 96556.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054030 restraints weight = 68040.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054636 restraints weight = 53636.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055107 restraints weight = 46188.263| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30394 Z= 0.132 Angle : 0.672 13.402 41257 Z= 0.318 Chirality : 0.038 0.218 4660 Planarity : 0.005 0.114 5152 Dihedral : 7.074 59.913 4944 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.31 % Allowed : 27.62 % Favored : 69.07 % 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: 0.78 (0.15), residues: 3640 helix: 1.91 (0.11), residues: 2464 sheet: -2.75 (0.38), residues: 148 loop : -2.57 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 437 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 0.00298 / 0.13 (30392) covalent geometry : angle 0.67183 / 0.32 (41236) SS BOND : bond 0.00139 / 0.07 ( 2) SS BOND : angle 0.05592 / 0.04 ( 21) hydrogen bonds : bond 0.03158 / 2.15 ( 1724) hydrogen bonds : angle 4.03112 / 2.91 ( 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 313 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 212 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8229 (mmm) cc_final: 0.7852 (mmp) REVERT: A 225 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7735 (mm) REVERT: A 284 MET cc_start: 0.8192 (mmt) cc_final: 0.7572 (ptm) REVERT: A 410 GLN cc_start: 0.9592 (tp-100) cc_final: 0.9340 (tp-100) REVERT: A 562 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9364 (tp) REVERT: A 641 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9332 (tt) REVERT: A 900 MET cc_start: 0.9346 (mmm) cc_final: 0.9013 (tpt) REVERT: A 1156 ASP cc_start: 0.9104 (m-30) cc_final: 0.8716 (m-30) REVERT: A 1168 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 1170 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8808 (pp30) REVERT: B 186 MET cc_start: 0.8497 (mmm) cc_final: 0.8064 (mmm) REVERT: B 284 MET cc_start: 0.8072 (mmt) cc_final: 0.7627 (mmp) REVERT: B 414 PHE cc_start: 0.8439 (t80) cc_final: 0.8210 (t80) REVERT: B 562 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9501 (tp) REVERT: B 580 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8642 (mt-10) REVERT: B 641 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9329 (tt) REVERT: B 1150 ARG cc_start: 0.9471 (OUTLIER) cc_final: 0.8870 (mtm110) REVERT: B 1168 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.6791 (t80) REVERT: C 186 MET cc_start: 0.8154 (mmm) cc_final: 0.7687 (mmm) REVERT: C 225 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7628 (mm) REVERT: C 284 MET cc_start: 0.8118 (mmt) cc_final: 0.7683 (mmp) REVERT: C 414 PHE cc_start: 0.8398 (t80) cc_final: 0.8192 (t80) REVERT: C 562 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9504 (tp) REVERT: C 580 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 641 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9327 (tt) REVERT: C 1038 LEU cc_start: 0.9711 (tt) cc_final: 0.9498 (tp) REVERT: C 1146 GLU cc_start: 0.9375 (tp30) cc_final: 0.8755 (tp30) REVERT: C 1156 ASP cc_start: 0.9098 (m-30) cc_final: 0.8777 (m-30) REVERT: C 1170 GLN cc_start: 0.8573 (pp30) cc_final: 0.8213 (pp30) REVERT: D 186 MET cc_start: 0.8203 (mmm) cc_final: 0.7621 (mmp) REVERT: D 284 MET cc_start: 0.8171 (mmt) cc_final: 0.7547 (ptm) REVERT: D 410 GLN cc_start: 0.9553 (tp-100) cc_final: 0.9331 (tp-100) REVERT: D 414 PHE cc_start: 0.8478 (t80) cc_final: 0.8168 (t80) REVERT: D 562 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9354 (tp) REVERT: D 580 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8656 (mt-10) REVERT: D 641 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9320 (tt) REVERT: D 1168 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7172 (t80) outliers start: 101 outliers final: 84 residues processed: 308 average time/residue: 0.1519 time to fit residues: 82.5200 Evaluate side-chains 309 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 211 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR 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 225 LEU 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 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 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 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 375 THR 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 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 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 1088 LEU Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 138 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 433 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 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 1025 VAL Chi-restraints excluded: chain C residue 1088 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 443 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 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 858 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 1025 VAL 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: chunk 209 optimal weight: 0.0980 chunk 263 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 336 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1037 ASN D1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.066740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051915 restraints weight = 166233.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053344 restraints weight = 96865.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054324 restraints weight = 68202.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054977 restraints weight = 53775.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.055389 restraints weight = 45952.026| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30394 Z= 0.117 Angle : 0.667 12.348 41257 Z= 0.312 Chirality : 0.038 0.281 4660 Planarity : 0.005 0.101 5152 Dihedral : 6.996 58.445 4944 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.64 % Allowed : 27.29 % Favored : 69.07 % 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: 1.91 (0.11), residues: 2456 sheet: -2.74 (0.38), residues: 148 loop : -2.60 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 113 TYR 0.009 0.001 TYR D 256 PHE 0.013 0.001 PHE A 627 TRP 0.017 0.001 TRP A 152 HIS 0.002 0.001 HIS B 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (30392) covalent geometry : angle 0.66716 / 0.31 (41236) SS BOND : bond 0.00089 / 0.04 ( 2) SS BOND : angle 0.07623 / 0.05 ( 21) hydrogen bonds : bond 0.03042 / 2.08 ( 1724) hydrogen bonds : angle 3.99934 / 2.88 ( 5148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4709.27 seconds wall clock time: 82 minutes 22.36 seconds (4942.36 seconds total)