Starting phenix.real_space_refine on Wed Nov 20 06:56:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xff_38303/11_2024/8xff_38303.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xff_38303/11_2024/8xff_38303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xff_38303/11_2024/8xff_38303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xff_38303/11_2024/8xff_38303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xff_38303/11_2024/8xff_38303.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xff_38303/11_2024/8xff_38303.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 13713 2.51 5 N 3441 2.21 5 O 3914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21142 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1129 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7844 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 19, 'TRANS': 963} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 27, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7778 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 19, 'TRANS': 964} Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 11, 'ASP:plan': 21, 'PHE:plan': 1, 'GLU:plan': 34, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 275 Chain: "D" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2224 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 266} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2167 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 267} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 12.62, per 1000 atoms: 0.60 Number of scatterers: 21142 At special positions: 0 Unit cell: (98.8, 127.4, 185.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 3914 8.00 N 3441 7.00 C 13713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.67 Conformation dependent library (CDL) restraints added in 2.9 seconds 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 10 sheets defined 57.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.842A pdb=" N GLU A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 removed outlier: 4.304A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.579A pdb=" N ASP A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 removed outlier: 4.162A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.516A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.248A pdb=" N ILE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.090A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.600A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.543A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.513A pdb=" N TRP A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.542A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 4.025A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.774A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.645A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.965A pdb=" N LYS A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.618A pdb=" N ARG A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.939A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.800A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.872A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 440 " --> pdb=" O TYR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 468 through 489 removed outlier: 3.548A pdb=" N ASN A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.764A pdb=" N GLU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.467A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.541A pdb=" N GLU A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.515A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.740A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 627 removed outlier: 3.573A pdb=" N LEU A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.617A pdb=" N SER A 637 " --> pdb=" O LEU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 removed outlier: 3.742A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.613A pdb=" N ASN A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 682 through 700 removed outlier: 3.705A pdb=" N GLU A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 removed outlier: 5.125A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.841A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'A' and resid 768 through 785 removed outlier: 3.863A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 780 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.710A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 832 through 840 removed outlier: 3.874A pdb=" N ASP A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.648A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 902 removed outlier: 3.631A pdb=" N LEU A 884 " --> pdb=" O GLU A 880 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.731A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.655A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 927 through 931' Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.588A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.564A pdb=" N TRP A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 959 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 973 through 989 removed outlier: 4.110A pdb=" N HIS A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 981 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 25 through 38 removed outlier: 3.598A pdb=" N ILE B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.847A pdb=" N LYS B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 71 " --> pdb=" O HIS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 85 Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.748A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.636A pdb=" N LEU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.644A pdb=" N CYS B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.575A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 197 through 210 removed outlier: 3.966A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 281 through 299 removed outlier: 3.665A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 3.591A pdb=" N TYR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.963A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 366 removed outlier: 4.687A pdb=" N PHE B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 391 removed outlier: 4.583A pdb=" N ASN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.696A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 440 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 460 Processing helix chain 'B' and resid 468 through 487 removed outlier: 3.752A pdb=" N TYR B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.597A pdb=" N PHE B 500 " --> pdb=" O GLY B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.507A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.794A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 547 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 removed outlier: 4.418A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.548A pdb=" N LEU B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 625 removed outlier: 3.535A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.725A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 639' Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.799A pdb=" N LEU B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 686 through 700 removed outlier: 3.683A pdb=" N GLY B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 698 " --> pdb=" O GLU B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 722 removed outlier: 3.690A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.873A pdb=" N LYS B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 760 removed outlier: 3.707A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 763 No H-bonds generated for 'chain 'B' and resid 761 through 763' Processing helix chain 'B' and resid 768 through 784 removed outlier: 4.577A pdb=" N ILE B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 777 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 810 removed outlier: 3.832A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 825 removed outlier: 3.642A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.649A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 4.260A pdb=" N SER B 851 " --> pdb=" O THR B 847 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 868 Processing helix chain 'B' and resid 880 through 901 removed outlier: 3.814A pdb=" N ILE B 885 " --> pdb=" O HIS B 881 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 886 " --> pdb=" O GLU B 882 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 896 " --> pdb=" O ARG B 892 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE B 897 " --> pdb=" O LYS B 893 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.693A pdb=" N PHE B 916 " --> pdb=" O TYR B 912 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 917 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.709A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.735A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 960 removed outlier: 3.713A pdb=" N LEU B 959 " --> pdb=" O PRO B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 removed outlier: 3.692A pdb=" N LEU B 967 " --> pdb=" O ASN B 963 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 986 removed outlier: 4.376A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 981 " --> pdb=" O LYS B 977 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.660A pdb=" N MET B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.543A pdb=" N GLU D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 82 through 96 Proline residue: D 88 - end of helix removed outlier: 3.726A pdb=" N ASN D 93 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.877A pdb=" N ILE D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 123 removed outlier: 4.118A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.848A pdb=" N ARG D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 removed outlier: 4.379A pdb=" N LYS D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.589A pdb=" N TYR D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.708A pdb=" N ILE D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 275' Processing helix chain 'D' and resid 281 through 299 removed outlier: 3.951A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 294 " --> pdb=" O MET D 290 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 40 removed outlier: 3.860A pdb=" N THR E 34 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.340A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 54' Processing helix chain 'E' and resid 58 through 72 removed outlier: 3.750A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.968A pdb=" N ILE E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.635A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 138 through 146 removed outlier: 3.598A pdb=" N CYS E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 144 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.556A pdb=" N ASP E 157 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.519A pdb=" N TYR E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.652A pdb=" N ASN E 202 " --> pdb=" O PRO E 198 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 removed outlier: 3.591A pdb=" N ASN E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.855A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE E 294 " --> pdb=" O MET E 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.528A pdb=" N ASP C 10 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN C 255 " --> pdb=" O PHE B 907 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 907 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 244 through 246 removed outlier: 4.316A pdb=" N ILE C 36 " --> pdb=" O TYR A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.564A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 216 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.862A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 130 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA8, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.266A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 129 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 152 removed outlier: 5.612A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ILE E 130 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 213 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE E 246 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE E 215 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) 801 hydrogen bonds defined for protein. 2292 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: 8.66 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5611 1.33 - 1.45: 4836 1.45 - 1.57: 11070 1.57 - 1.69: 1 1.69 - 1.81: 124 Bond restraints: 21642 Sorted by residual: bond pdb=" CA LEU A 167 " pdb=" CB LEU A 167 " ideal model delta sigma weight residual 1.529 1.449 0.080 1.34e-02 5.57e+03 3.54e+01 bond pdb=" C ASP D 111 " pdb=" N LYS D 112 " ideal model delta sigma weight residual 1.327 1.228 0.098 1.71e-02 3.42e+03 3.31e+01 bond pdb=" C LEU A 842 " pdb=" N PRO A 843 " ideal model delta sigma weight residual 1.334 1.367 -0.033 8.40e-03 1.42e+04 1.57e+01 bond pdb=" CA SER C 37 " pdb=" CB SER C 37 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.54e-02 4.22e+03 8.90e+00 bond pdb=" CG PRO B 318 " pdb=" CD PRO B 318 " ideal model delta sigma weight residual 1.503 1.402 0.101 3.40e-02 8.65e+02 8.75e+00 ... (remaining 21637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 28105 2.41 - 4.82: 1080 4.82 - 7.23: 115 7.23 - 9.64: 28 9.64 - 12.05: 2 Bond angle restraints: 29330 Sorted by residual: angle pdb=" N GLU A 560 " pdb=" CA GLU A 560 " pdb=" C GLU A 560 " ideal model delta sigma weight residual 113.19 104.63 8.56 1.19e+00 7.06e-01 5.18e+01 angle pdb=" N GLU B 298 " pdb=" CA GLU B 298 " pdb=" C GLU B 298 " ideal model delta sigma weight residual 111.02 103.16 7.86 1.22e+00 6.72e-01 4.15e+01 angle pdb=" C ARG D 86 " pdb=" N ILE D 87 " pdb=" CA ILE D 87 " ideal model delta sigma weight residual 120.24 124.06 -3.82 6.30e-01 2.52e+00 3.67e+01 angle pdb=" N VAL B 988 " pdb=" CA VAL B 988 " pdb=" C VAL B 988 " ideal model delta sigma weight residual 112.96 107.02 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" N SER C 33 " pdb=" CA SER C 33 " pdb=" C SER C 33 " ideal model delta sigma weight residual 110.80 98.75 12.05 2.13e+00 2.20e-01 3.20e+01 ... (remaining 29325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 11891 15.41 - 30.83: 670 30.83 - 46.24: 147 46.24 - 61.65: 17 61.65 - 77.06: 14 Dihedral angle restraints: 12739 sinusoidal: 4840 harmonic: 7899 Sorted by residual: dihedral pdb=" CA PHE A 699 " pdb=" C PHE A 699 " pdb=" N SER A 700 " pdb=" CA SER A 700 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER A 570 " pdb=" C SER A 570 " pdb=" N GLU A 571 " pdb=" CA GLU A 571 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU B 624 " pdb=" C GLU B 624 " pdb=" N TYR B 625 " pdb=" CA TYR B 625 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 12736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2748 0.094 - 0.188: 456 0.188 - 0.282: 21 0.282 - 0.376: 4 0.376 - 0.470: 2 Chirality restraints: 3231 Sorted by residual: chirality pdb=" CB ILE C 235 " pdb=" CA ILE C 235 " pdb=" CG1 ILE C 235 " pdb=" CG2 ILE C 235 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" CB ILE B 216 " pdb=" CA ILE B 216 " pdb=" CG1 ILE B 216 " pdb=" CG2 ILE B 216 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CB ILE A 407 " pdb=" CA ILE A 407 " pdb=" CG1 ILE A 407 " pdb=" CG2 ILE A 407 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3228 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 678 " 0.024 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE A 678 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 678 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 678 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 678 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 678 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 678 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1003 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C TYR A1003 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR A1003 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE A1004 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 804 " -0.024 2.00e-02 2.50e+03 2.00e-02 8.00e+00 pdb=" CG TYR B 804 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 804 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 804 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 804 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 804 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 804 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 804 " -0.007 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4387 2.76 - 3.29: 19596 3.29 - 3.83: 34108 3.83 - 4.36: 42567 4.36 - 4.90: 70025 Nonbonded interactions: 170683 Sorted by model distance: nonbonded pdb=" O GLN C 34 " pdb=" N ILE C 36 " model vdw 2.224 3.120 nonbonded pdb=" OH TYR B 709 " pdb=" OD2 ASP B 748 " model vdw 2.225 3.040 nonbonded pdb=" O HIS A 852 " pdb=" OG SER A 855 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR B 920 " pdb=" OE2 GLU B 931 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR B 324 " pdb=" OD1 ASP B 590 " model vdw 2.265 3.040 ... (remaining 170678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 or (resid 25 and (name N or name CA or name C or name O or name C \ B )) or resid 26 through 27 or (resid 28 and (name N or name CA or name C or nam \ e O or name CB )) or resid 29 through 54 or (resid 55 and (name N or name CA or \ name C or name O or name CB )) or resid 56 through 60 or (resid 61 and (name N o \ r name CA or name C or name O or name CB )) or resid 62 through 110 or (resid 11 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 112 through \ 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or re \ sid 120 through 124 or (resid 125 and (name N or name CA or name C or name O or \ name CB )) or resid 126 through 143 or (resid 144 and (name N or name CA or name \ C or name O or name CB )) or resid 145 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB )) or resid 148 through 187 or (resid 18 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 189 through \ 193 or (resid 194 through 195 and (name N or name CA or name C or name O or name \ CB )) or resid 196 through 226 or (resid 227 and (name N or name CA or name C o \ r name O or name CB )) or resid 228 through 229 or (resid 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 236 or (resid 237 th \ rough 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 253 or (resid 254 through 256 and (name N or name CA or name C or name O \ or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 261 or (resid 262 through 26 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 264 through \ 299 or (resid 300 and (name N or name CA or name C or name O or name CB )) or re \ sid 301 through 330 or (resid 331 and (name N or name CA or name C or name O or \ name CB )) or resid 332 through 347 or (resid 348 and (name N or name CA or name \ C or name O or name CB )) or resid 349 through 375 or (resid 376 and (name N or \ name CA or name C or name O or name CB )) or resid 377 through 393 or (resid 39 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 395 through \ 397 or (resid 398 through 400 and (name N or name CA or name C or name O or name \ CB )) or resid 401 through 402 or (resid 403 through 404 and (name N or name CA \ or name C or name O or name CB )) or resid 405 through 422 or (resid 423 and (n \ ame N or name CA or name C or name O or name CB )) or resid 424 through 425 or ( \ resid 426 and (name N or name CA or name C or name O or name CB )) or resid 427 \ or (resid 428 and (name N or name CA or name C or name O or name CB )) or resid \ 429 through 432 or (resid 433 and (name N or name CA or name C or name O or name \ CB )) or resid 434 through 441 or (resid 442 through 443 and (name N or name CA \ or name C or name O or name CB )) or resid 444 through 448 or (resid 449 and (n \ ame N or name CA or name C or name O or name CB )) or resid 450 through 507 or ( \ resid 508 through 510 and (name N or name CA or name C or name O or name CB )) o \ r resid 511 through 515 or (resid 516 and (name N or name CA or name C or name O \ or name CB )) or resid 517 through 519 or (resid 520 through 521 and (name N or \ name CA or name C or name O or name CB )) or resid 522 through 533 or (resid 53 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 535 through \ 539 or (resid 540 and (name N or name CA or name C or name O or name CB )) or re \ sid 541 through 542 or (resid 543 and (name N or name CA or name C or name O or \ name CB )) or resid 544 through 552 or (resid 553 and (name N or name CA or name \ C or name O or name CB )) or resid 554 through 558 or (resid 559 through 560 an \ d (name N or name CA or name C or name O or name CB )) or resid 561 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 577 or (resid 578 and (name N or name CA or name C or name O or name \ CB )) or resid 579 through 606 or (resid 607 and (name N or name CA or name C o \ r name O or name CB )) or resid 608 through 620 or (resid 621 and (name N or nam \ e CA or name C or name O or name CB )) or resid 622 through 647 or (resid 648 an \ d (name N or name CA or name C or name O or name CB )) or resid 649 through 674 \ or (resid 675 and (name N or name CA or name C or name O or name CB )) or resid \ 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) or re \ sid 678 through 684 or (resid 685 through 686 and (name N or name CA or name C o \ r name O or name CB )) or resid 687 through 693 or (resid 694 and (name N or nam \ e CA or name C or name O or name CB )) or resid 695 through 696 or (resid 697 an \ d (name N or name CA or name C or name O or name CB )) or resid 698 through 726 \ or (resid 727 and (name N or name CA or name C or name O or name CB )) or resid \ 728 through 729 or (resid 730 through 731 and (name N or name CA or name C or na \ me O or name CB )) or resid 732 through 737 or (resid 738 through 739 and (name \ N or name CA or name C or name O or name CB )) or resid 740 through 745 or (resi \ d 746 and (name N or name CA or name C or name O or name CB )) or resid 747 thro \ ugh 783 or (resid 784 and (name N or name CA or name C or name O or name CB )) o \ r resid 785 through 788 or (resid 789 through 790 and (name N or name CA or name \ C or name O or name CB )) or resid 791 through 817 or (resid 818 and (name N or \ name CA or name C or name O or name CB )) or resid 819 through 821 or (resid 82 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 823 through \ 835 or (resid 836 and (name N or name CA or name C or name O or name CB )) or re \ sid 837 through 846 or (resid 847 through 849 and (name N or name CA or name C o \ r name O or name CB )) or resid 850 through 857 or (resid 858 and (name N or nam \ e CA or name C or name O or name CB )) or resid 859 through 862 or (resid 863 th \ rough 864 and (name N or name CA or name C or name O or name CB )) or resid 865 \ through 874 or (resid 875 through 876 and (name N or name CA or name C or name O \ or name CB )) or resid 877 through 964 or (resid 965 and (name N or name CA or \ name C or name O or name CB )) or resid 966 through 1005)) selection = (chain 'B' and (resid 23 through 81 or (resid 82 through 83 and (name N or name \ CA or name C or name O or name CB )) or resid 84 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 297 or \ (resid 298 and (name N or name CA or name C or name O or name CB )) or resid 299 \ through 463 or (resid 464 and (name N or name CA or name C or name O or name CB \ )) or resid 465 through 502 or (resid 503 through 505 and (name N or name CA or \ name C or name O or name CB )) or resid 506 through 525 or (resid 526 and (name \ N or name CA or name C or name O or name CB )) or resid 527 through 570 or (res \ id 571 and (name N or name CA or name C or name O or name CB )) or resid 572 thr \ ough 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) \ or resid 628 or (resid 629 and (name N or name CA or name C or name O or name CB \ )) or resid 630 through 758 or (resid 759 and (name N or name CA or name C or n \ ame O or name CB )) or resid 760 through 765 or (resid 766 and (name N or name C \ A or name C or name O or name CB )) or resid 767 through 811 or (resid 812 throu \ gh 814 and (name N or name CA or name C or name O or name CB )) or resid 815 thr \ ough 828 or (resid 829 through 833 and (name N or name CA or name C or name O or \ name CB )) or resid 834 through 856 or (resid 857 through 858 and (name N or na \ me CA or name C or name O or name CB )) or resid 859 through 873 or (resid 874 t \ hrough 876 and (name N or name CA or name C or name O or name CB )) or resid 877 \ through 879 or (resid 880 and (name N or name CA or name C or name O or name CB \ )) or resid 881 or (resid 882 through 884 and (name N or name CA or name C or n \ ame O or name CB )) or resid 885 through 889 or (resid 890 and (name N or name C \ A or name C or name O or name CB )) or resid 891 or (resid 892 through 893 and ( \ name N or name CA or name C or name O or name CB )) or resid 894 through 895 or \ (resid 896 and (name N or name CA or name C or name O or name CB )) or resid 897 \ through 899 or (resid 900 through 902 and (name N or name CA or name C or name \ O or name CB )) or resid 903 or (resid 904 through 907 and (name N or name CA or \ name C or name O or name CB )) or resid 908 through 909 or (resid 910 and (name \ N or name CA or name C or name O or name CB )) or resid 911 through 922 or (res \ id 923 and (name N or name CA or name C or name O or name CB )) or resid 924 thr \ ough 925 or (resid 926 and (name N or name CA or name C or name O or name CB )) \ or resid 927 through 928 or (resid 929 and (name N or name CA or name C or name \ O or name CB )) or resid 930 or (resid 931 through 934 and (name N or name CA or \ name C or name O or name CB )) or resid 935 or (resid 936 and (name N or name C \ A or name C or name O or name CB )) or resid 937 through 947 or (resid 948 and ( \ name N or name CA or name C or name O or name CB )) or resid 949 through 952 or \ (resid 953 and (name N or name CA or name C or name O or name CB )) or resid 954 \ through 968 or (resid 969 and (name N or name CA or name C or name O or name CB \ )) or resid 970 through 972 or (resid 973 through 974 and (name N or name CA or \ name C or name O or name CB )) or resid 975 or (resid 976 and (name N or name C \ A or name C or name O or name CB )) or resid 977 through 981 or (resid 982 and ( \ name N or name CA or name C or name O or name CB )) or resid 983 through 985 or \ (resid 986 and (name N or name CA or name C or name O or name CB )) or resid 987 \ through 1005)) } ncs_group { reference = (chain 'D' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 or (resid 25 and (name N or name CA or name C or name O or name C \ B )) or resid 26 through 27 or (resid 28 and (name N or name CA or name C or nam \ e O or name CB )) or resid 29 through 54 or (resid 55 and (name N or name CA or \ name C or name O or name CB )) or resid 56 through 60 or (resid 61 and (name N o \ r name CA or name C or name O or name CB )) or resid 62 through 110 or (resid 11 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 112 through \ 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or re \ sid 120 through 124 or (resid 125 and (name N or name CA or name C or name O or \ name CB )) or resid 126 through 143 or (resid 144 and (name N or name CA or name \ C or name O or name CB )) or resid 145 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB )) or resid 148 through 187 or (resid 18 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 189 through \ 193 or (resid 194 through 195 and (name N or name CA or name C or name O or name \ CB )) or resid 196 through 226 or (resid 227 and (name N or name CA or name C o \ r name O or name CB )) or resid 228 through 229 or (resid 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 236 or (resid 237 th \ rough 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 253 or (resid 254 through 256 and (name N or name CA or name C or name O \ or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 261 or (resid 262 through 26 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 264 through \ 299)) selection = (chain 'E' and (resid 23 through 81 or (resid 82 through 83 and (name N or name \ CA or name C or name O or name CB )) or resid 84 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 297 or \ (resid 298 and (name N or name CA or name C or name O or name CB )) or resid 299 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 47.590 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.012 0.118 21642 Z= 0.772 Angle : 1.071 12.054 29330 Z= 0.621 Chirality : 0.068 0.470 3231 Planarity : 0.007 0.069 3738 Dihedral : 11.055 77.063 7669 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.09 % Favored : 93.72 % Rotamer: Outliers : 0.87 % Allowed : 3.84 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.12), residues: 2658 helix: -4.18 (0.07), residues: 1391 sheet: -2.82 (0.50), residues: 75 loop : -2.50 (0.15), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 601 HIS 0.021 0.004 HIS D 118 PHE 0.060 0.004 PHE A 678 TYR 0.044 0.004 TYR C 192 ARG 0.018 0.002 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 462 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 TYR cc_start: 0.8505 (m-10) cc_final: 0.7876 (m-10) REVERT: C 23 PHE cc_start: 0.7532 (m-80) cc_final: 0.6940 (m-10) REVERT: A 559 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: A 863 ASN cc_start: 0.9010 (m-40) cc_final: 0.8801 (m110) REVERT: B 191 LEU cc_start: 0.7946 (mp) cc_final: 0.7607 (mt) REVERT: B 447 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8283 (mtm-85) REVERT: D 124 MET cc_start: 0.8613 (mmm) cc_final: 0.8159 (mmp) REVERT: E 212 THR cc_start: 0.9035 (m) cc_final: 0.8676 (p) outliers start: 19 outliers final: 5 residues processed: 477 average time/residue: 0.3856 time to fit residues: 272.0954 Evaluate side-chains 224 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 859 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 93 ASN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 226 ASN A 255 ASN A 332 HIS A 339 HIS A 351 ASN A 391 ASN A 404 ASN A 606 HIS A 609 HIS B 67 HIS B 89 GLN B 93 ASN B 377 GLN B 491 GLN ** B 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS B 829 GLN B 881 HIS B 927 ASN B 978 HIS D 89 GLN D 93 ASN D 125 ASN D 202 ASN E 89 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21642 Z= 0.186 Angle : 0.621 11.586 29330 Z= 0.328 Chirality : 0.043 0.360 3231 Planarity : 0.004 0.052 3738 Dihedral : 6.146 89.116 2936 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % Rotamer: Outliers : 1.74 % Allowed : 9.27 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.14), residues: 2658 helix: -2.22 (0.11), residues: 1381 sheet: -3.27 (0.41), residues: 87 loop : -1.82 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 143 HIS 0.007 0.001 HIS D 118 PHE 0.029 0.001 PHE A 916 TYR 0.023 0.001 TYR C 192 ARG 0.006 0.001 ARG B 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 PHE cc_start: 0.7546 (m-80) cc_final: 0.7126 (m-10) REVERT: A 559 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: A 912 TYR cc_start: 0.8730 (m-10) cc_final: 0.8436 (m-80) REVERT: A 916 PHE cc_start: 0.9079 (m-80) cc_final: 0.8638 (m-80) REVERT: B 526 ASP cc_start: 0.7130 (p0) cc_final: 0.6807 (p0) REVERT: D 238 ASP cc_start: 0.7088 (t0) cc_final: 0.6746 (t0) outliers start: 38 outliers final: 12 residues processed: 286 average time/residue: 0.3612 time to fit residues: 157.7619 Evaluate side-chains 208 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain E residue 293 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 0.4980 chunk 259 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 125 ASN B 503 HIS B 548 ASN B 563 ASN D 202 ASN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21642 Z= 0.175 Angle : 0.549 10.921 29330 Z= 0.286 Chirality : 0.042 0.291 3231 Planarity : 0.003 0.049 3738 Dihedral : 5.142 55.212 2927 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 1.74 % Allowed : 10.60 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 2658 helix: -1.05 (0.13), residues: 1382 sheet: -2.21 (0.43), residues: 104 loop : -1.54 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 143 HIS 0.012 0.001 HIS A 339 PHE 0.032 0.001 PHE C 195 TYR 0.017 0.001 TYR D 223 ARG 0.010 0.001 ARG D 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 PHE cc_start: 0.7566 (m-80) cc_final: 0.7346 (m-80) REVERT: A 559 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: A 916 PHE cc_start: 0.8968 (m-80) cc_final: 0.8463 (m-80) REVERT: D 238 ASP cc_start: 0.6977 (t0) cc_final: 0.6607 (t0) REVERT: E 124 MET cc_start: 0.8559 (mmm) cc_final: 0.8279 (mmm) outliers start: 38 outliers final: 19 residues processed: 224 average time/residue: 0.3801 time to fit residues: 131.8289 Evaluate side-chains 202 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 20.0000 chunk 180 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 810 HIS A 990 ASN B 391 ASN B 606 HIS B 614 ASN ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN D 115 ASN D 118 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21642 Z= 0.317 Angle : 0.586 10.244 29330 Z= 0.306 Chirality : 0.043 0.247 3231 Planarity : 0.004 0.074 3738 Dihedral : 5.005 51.935 2927 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 2.19 % Allowed : 10.60 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2658 helix: -0.44 (0.14), residues: 1401 sheet: -1.84 (0.49), residues: 102 loop : -1.30 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 143 HIS 0.008 0.001 HIS D 118 PHE 0.021 0.002 PHE C 204 TYR 0.019 0.002 TYR C 192 ARG 0.007 0.001 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: A 916 PHE cc_start: 0.8994 (m-80) cc_final: 0.8416 (m-80) REVERT: A 930 MET cc_start: 0.7928 (ptp) cc_final: 0.7698 (ptp) REVERT: D 115 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7260 (p0) REVERT: D 238 ASP cc_start: 0.6992 (t0) cc_final: 0.6671 (t0) outliers start: 48 outliers final: 26 residues processed: 218 average time/residue: 0.3587 time to fit residues: 121.1279 Evaluate side-chains 199 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain E residue 36 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 130 optimal weight: 0.0980 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 789 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21642 Z= 0.173 Angle : 0.531 11.387 29330 Z= 0.273 Chirality : 0.041 0.266 3231 Planarity : 0.003 0.048 3738 Dihedral : 4.781 50.565 2927 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 1.78 % Allowed : 11.56 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2658 helix: 0.02 (0.14), residues: 1401 sheet: -1.68 (0.47), residues: 108 loop : -1.13 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 143 HIS 0.014 0.001 HIS D 118 PHE 0.033 0.001 PHE C 195 TYR 0.016 0.001 TYR C 192 ARG 0.005 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: A 912 TYR cc_start: 0.8732 (m-80) cc_final: 0.8487 (m-80) REVERT: A 913 MET cc_start: 0.8585 (ptp) cc_final: 0.8370 (ptp) REVERT: A 916 PHE cc_start: 0.8992 (m-80) cc_final: 0.8363 (m-80) REVERT: A 930 MET cc_start: 0.7968 (ptp) cc_final: 0.7582 (ptp) REVERT: B 987 ARG cc_start: 0.8519 (mmp-170) cc_final: 0.8245 (mmp-170) REVERT: D 238 ASP cc_start: 0.6917 (t0) cc_final: 0.6401 (t0) outliers start: 39 outliers final: 33 residues processed: 214 average time/residue: 0.3657 time to fit residues: 121.8129 Evaluate side-chains 204 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.5980 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 118 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 21642 Z= 0.147 Angle : 0.508 10.142 29330 Z= 0.262 Chirality : 0.041 0.281 3231 Planarity : 0.003 0.051 3738 Dihedral : 4.571 49.656 2927 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.78 % Allowed : 12.47 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2658 helix: 0.34 (0.14), residues: 1389 sheet: -1.64 (0.47), residues: 108 loop : -1.00 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 143 HIS 0.009 0.001 HIS D 118 PHE 0.026 0.001 PHE C 195 TYR 0.011 0.001 TYR D 66 ARG 0.006 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 PHE cc_start: 0.7508 (m-80) cc_final: 0.7127 (m-80) REVERT: C 67 PHE cc_start: 0.7018 (p90) cc_final: 0.5627 (p90) REVERT: A 559 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: A 912 TYR cc_start: 0.8692 (m-80) cc_final: 0.8463 (m-80) REVERT: A 913 MET cc_start: 0.8610 (ptp) cc_final: 0.8363 (ptp) REVERT: A 916 PHE cc_start: 0.8975 (m-80) cc_final: 0.8415 (m-80) REVERT: A 930 MET cc_start: 0.7953 (ptp) cc_final: 0.7699 (ptp) outliers start: 39 outliers final: 28 residues processed: 217 average time/residue: 0.3781 time to fit residues: 127.1196 Evaluate side-chains 196 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21642 Z= 0.263 Angle : 0.561 10.542 29330 Z= 0.288 Chirality : 0.042 0.306 3231 Planarity : 0.003 0.057 3738 Dihedral : 4.626 50.460 2927 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 1.74 % Allowed : 12.84 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2658 helix: 0.42 (0.14), residues: 1402 sheet: -1.66 (0.47), residues: 106 loop : -0.86 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 143 HIS 0.008 0.001 HIS D 118 PHE 0.023 0.001 PHE C 195 TYR 0.015 0.001 TYR B 755 ARG 0.009 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 2.446 Fit side-chains revert: symmetry clash REVERT: C 67 PHE cc_start: 0.7248 (p90) cc_final: 0.6855 (p90) REVERT: A 559 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7444 (m-10) REVERT: A 912 TYR cc_start: 0.8774 (m-80) cc_final: 0.8493 (m-80) REVERT: A 913 MET cc_start: 0.8649 (ptp) cc_final: 0.8369 (ptp) REVERT: A 916 PHE cc_start: 0.8916 (m-80) cc_final: 0.8258 (m-80) REVERT: A 930 MET cc_start: 0.7902 (ptp) cc_final: 0.7652 (ptp) REVERT: D 244 PHE cc_start: 0.7321 (m-80) cc_final: 0.6860 (m-10) outliers start: 38 outliers final: 28 residues processed: 191 average time/residue: 0.3784 time to fit residues: 110.7970 Evaluate side-chains 188 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 231 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21642 Z= 0.270 Angle : 0.567 9.996 29330 Z= 0.292 Chirality : 0.042 0.323 3231 Planarity : 0.003 0.052 3738 Dihedral : 4.592 51.626 2925 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.74 % Allowed : 13.02 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2658 helix: 0.54 (0.14), residues: 1406 sheet: -1.68 (0.47), residues: 106 loop : -0.80 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 143 HIS 0.006 0.001 HIS D 118 PHE 0.020 0.001 PHE C 195 TYR 0.014 0.001 TYR B 755 ARG 0.009 0.000 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.8277 (tpt-90) cc_final: 0.8067 (tpt-90) REVERT: A 559 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: A 912 TYR cc_start: 0.8775 (m-80) cc_final: 0.8487 (m-80) REVERT: A 913 MET cc_start: 0.8646 (ptp) cc_final: 0.8363 (ptp) REVERT: A 916 PHE cc_start: 0.8838 (m-80) cc_final: 0.8171 (m-80) REVERT: A 930 MET cc_start: 0.7866 (ptp) cc_final: 0.7593 (ptp) REVERT: D 244 PHE cc_start: 0.7366 (m-80) cc_final: 0.7066 (m-10) outliers start: 38 outliers final: 30 residues processed: 189 average time/residue: 0.3621 time to fit residues: 104.8433 Evaluate side-chains 186 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.5980 chunk 222 optimal weight: 8.9990 chunk 237 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN C 255 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 21642 Z= 0.156 Angle : 0.539 11.215 29330 Z= 0.274 Chirality : 0.041 0.301 3231 Planarity : 0.003 0.053 3738 Dihedral : 4.480 51.927 2925 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 1.23 % Allowed : 13.52 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2658 helix: 0.74 (0.15), residues: 1403 sheet: -1.69 (0.47), residues: 108 loop : -0.74 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 143 HIS 0.004 0.001 HIS D 118 PHE 0.022 0.001 PHE C 204 TYR 0.011 0.001 TYR B 755 ARG 0.010 0.000 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: A 912 TYR cc_start: 0.8714 (m-80) cc_final: 0.8417 (m-80) REVERT: A 913 MET cc_start: 0.8619 (ptp) cc_final: 0.8314 (ptp) REVERT: A 916 PHE cc_start: 0.8806 (m-80) cc_final: 0.8126 (m-80) REVERT: A 930 MET cc_start: 0.7818 (ptp) cc_final: 0.7520 (ptp) REVERT: D 244 PHE cc_start: 0.7231 (m-80) cc_final: 0.6933 (m-10) REVERT: D 275 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8366 (mp) REVERT: E 165 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7434 (mtp85) outliers start: 27 outliers final: 19 residues processed: 186 average time/residue: 0.3661 time to fit residues: 104.7076 Evaluate side-chains 176 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 242 optimal weight: 0.3980 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 161 optimal weight: 0.3980 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 21642 Z= 0.145 Angle : 0.543 12.520 29330 Z= 0.274 Chirality : 0.041 0.291 3231 Planarity : 0.003 0.052 3738 Dihedral : 4.407 52.890 2925 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 1.01 % Allowed : 13.89 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2658 helix: 0.88 (0.15), residues: 1404 sheet: -1.74 (0.45), residues: 120 loop : -0.64 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 143 HIS 0.003 0.001 HIS D 118 PHE 0.020 0.001 PHE C 32 TYR 0.011 0.001 TYR A 920 ARG 0.009 0.000 ARG E 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7136 (m-10) REVERT: A 912 TYR cc_start: 0.8711 (m-80) cc_final: 0.8409 (m-80) REVERT: A 913 MET cc_start: 0.8560 (ptp) cc_final: 0.8245 (ptp) REVERT: A 916 PHE cc_start: 0.8783 (m-80) cc_final: 0.8121 (m-80) REVERT: A 930 MET cc_start: 0.7864 (ptp) cc_final: 0.7547 (ptp) REVERT: D 244 PHE cc_start: 0.7210 (m-80) cc_final: 0.6868 (m-10) REVERT: D 275 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8357 (mp) outliers start: 22 outliers final: 17 residues processed: 182 average time/residue: 0.3707 time to fit residues: 104.3016 Evaluate side-chains 172 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** 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 = 0.3652 r_free = 0.3652 target = 0.087878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058578 restraints weight = 63841.551| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.69 r_work: 0.2825 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21642 Z= 0.358 Angle : 0.634 13.144 29330 Z= 0.322 Chirality : 0.044 0.334 3231 Planarity : 0.003 0.056 3738 Dihedral : 4.587 54.003 2923 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 1.14 % Allowed : 13.80 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2658 helix: 0.74 (0.14), residues: 1406 sheet: -1.67 (0.46), residues: 116 loop : -0.60 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 143 HIS 0.005 0.001 HIS A 975 PHE 0.026 0.001 PHE C 32 TYR 0.017 0.001 TYR B 755 ARG 0.009 0.001 ARG E 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4415.86 seconds wall clock time: 82 minutes 7.59 seconds (4927.59 seconds total)