Starting phenix.real_space_refine on Sat Jun 21 13:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vur_43537/06_2025/8vur_43537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vur_43537/06_2025/8vur_43537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vur_43537/06_2025/8vur_43537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vur_43537/06_2025/8vur_43537.map" model { file = "/net/cci-nas-00/data/ceres_data/8vur_43537/06_2025/8vur_43537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vur_43537/06_2025/8vur_43537.cif" } resolution = 3.84 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= 0.016 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 111 5.16 5 C 15974 2.51 5 N 4354 2.21 5 O 4539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24978 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5778 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 33, 'TRANS': 753} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 277 Chain: "B" Number of atoms: 5547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5547 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 398 Chain: "C" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5496 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 33, 'TRANS': 753} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 749 Unresolved non-hydrogen angles: 921 Unresolved non-hydrogen dihedrals: 613 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 19, 'PHE:plan': 10, 'GLU:plan': 33, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 449 Chain: "D" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 5412 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 30, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 783 Unresolved non-hydrogen angles: 984 Unresolved non-hydrogen dihedrals: 641 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 29, 'PHE:plan': 12, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 447 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1456 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 159 Chain: "L" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1289 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 202 Time building chain proxies: 17.02, per 1000 atoms: 0.68 Number of scatterers: 24978 At special positions: 0 Unit cell: (128.4, 216.568, 187.464, 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 111 16.00 O 4539 8.00 N 4354 7.00 C 15974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 779 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 725 " - pdb=" SG CYS D 780 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 325 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 251 " - pdb=" SG CYS L 320 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 3.9 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6680 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 50 sheets defined 38.1% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 removed outlier: 4.120A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.623A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.375A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.630A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.038A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.623A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.955A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.064A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.507A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.728A pdb=" N ALA A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 580 Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 607 through 638 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.641A pdb=" N ILE A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 677 " --> pdb=" O TYR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 694 through 704 removed outlier: 3.502A pdb=" N ASP A 704 " --> pdb=" O GLN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 749 through 764 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.632A pdb=" N ASP A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 797 removed outlier: 3.516A pdb=" N GLY A 787 " --> pdb=" O GLU A 783 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL A 788 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU A 791 " --> pdb=" O GLY A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 813 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.606A pdb=" N ARG B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.085A pdb=" N ALA B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.561A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.658A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 4.134A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.802A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 311 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.652A pdb=" N ARG B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 removed outlier: 3.563A pdb=" N VAL B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.752A pdb=" N SER B 519 " --> pdb=" O ASN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 551 removed outlier: 3.889A pdb=" N GLU B 551 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 604 through 635 Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.781A pdb=" N ARG B 652 " --> pdb=" O LYS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 678 Processing helix chain 'B' and resid 678 through 686 removed outlier: 3.882A pdb=" N HIS B 682 " --> pdb=" O TYR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 703 Processing helix chain 'B' and resid 712 through 721 Processing helix chain 'B' and resid 751 through 766 removed outlier: 3.560A pdb=" N GLY B 766 " --> pdb=" O PHE B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 776 removed outlier: 3.679A pdb=" N GLU B 770 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 814 Processing helix chain 'C' and resid 35 through 53 Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.061A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.915A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.547A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 204 through 211 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.937A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.033A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 277 through 296 Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.658A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.651A pdb=" N GLY C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.992A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.787A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 580 Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.905A pdb=" N LEU C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 638 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 677 through 683 removed outlier: 3.739A pdb=" N MET C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 689 Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 764 through 774 Processing helix chain 'C' and resid 781 through 813 removed outlier: 3.950A pdb=" N VAL C 788 " --> pdb=" O ASN C 784 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET C 790 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU C 791 " --> pdb=" O GLY C 787 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE C 800 " --> pdb=" O ILE C 796 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE C 801 " --> pdb=" O VAL C 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.835A pdb=" N LEU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 107 through 119 removed outlier: 4.126A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.635A pdb=" N ALA D 131 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.674A pdb=" N GLN D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 287 through 311 removed outlier: 3.802A pdb=" N ARG D 291 " --> pdb=" O SER D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 443 through 447 Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 516 through 522 removed outlier: 4.032A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 522 " --> pdb=" O ARG D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 604 through 633 removed outlier: 3.621A pdb=" N MET D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 Processing helix chain 'D' and resid 668 through 678 removed outlier: 3.611A pdb=" N ARG D 672 " --> pdb=" O GLY D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 685 removed outlier: 3.842A pdb=" N TYR D 684 " --> pdb=" O TYR D 680 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET D 685 " --> pdb=" O MET D 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 680 through 685' Processing helix chain 'D' and resid 686 through 689 removed outlier: 4.222A pdb=" N ASN D 689 " --> pdb=" O THR D 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 686 through 689' Processing helix chain 'D' and resid 692 through 702 Processing helix chain 'D' and resid 712 through 721 Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 766 through 776 removed outlier: 3.848A pdb=" N GLU D 770 " --> pdb=" O GLY D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 814 removed outlier: 3.615A pdb=" N MET D 790 " --> pdb=" O ASP D 786 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.523A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.705A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing helix chain 'L' and resid 311 through 315 removed outlier: 3.567A pdb=" N GLU L 315 " --> pdb=" O THR L 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.503A pdb=" N LEU A 91 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.688A pdb=" N TYR A 330 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 338 " --> pdb=" O TYR A 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 removed outlier: 3.594A pdb=" N LEU A 398 " --> pdb=" O THR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.585A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 434 through 436 removed outlier: 3.580A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 455 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.675A pdb=" N VAL A 542 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.873A pdb=" N LEU B 40 " --> pdb=" O LEU B 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 124 through 125 removed outlier: 6.505A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 173 through 175 removed outlier: 7.651A pdb=" N THR B 174 " --> pdb=" O LEU B 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB7, first strand: chain 'B' and resid 277 through 281 removed outlier: 3.885A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 361 " --> pdb=" O TRP B 378 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP B 378 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB9, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AC1, first strand: chain 'B' and resid 417 through 419 removed outlier: 4.039A pdb=" N LYS B 454 " --> pdb=" O CYS B 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 533 through 536 removed outlier: 3.659A pdb=" N TYR B 710 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 708 " --> pdb=" O MET B 536 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 31 through 32 removed outlier: 7.027A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 168 removed outlier: 3.653A pdb=" N LEU C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.687A pdb=" N VAL C 249 " --> pdb=" O LEU C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 270 through 271 removed outlier: 6.731A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.658A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 401 through 402 Processing sheet with id=AD1, first strand: chain 'C' and resid 434 through 437 Processing sheet with id=AD2, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.515A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.625A pdb=" N VAL C 542 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 728 " --> pdb=" O VAL C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 124 through 125 removed outlier: 6.644A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 226 through 227 removed outlier: 3.652A pdb=" N ILE D 227 " --> pdb=" O PHE D 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.733A pdb=" N THR D 351 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.742A pdb=" N THR D 410 " --> pdb=" O TYR D 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 417 through 419 Processing sheet with id=AD9, first strand: chain 'D' and resid 437 through 439 Processing sheet with id=AE1, first strand: chain 'D' and resid 487 through 489 removed outlier: 3.813A pdb=" N LYS D 487 " --> pdb=" O ASN D 494 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN D 494 " --> pdb=" O LYS D 487 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 708 through 711 removed outlier: 3.524A pdb=" N TYR D 710 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 534 " --> pdb=" O TYR D 710 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 728 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.783A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS H 22 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 51 through 52 removed outlier: 3.502A pdb=" N TRP H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA H 97 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AE6, first strand: chain 'H' and resid 232 through 236 Processing sheet with id=AE7, first strand: chain 'H' and resid 232 through 236 Processing sheet with id=AE8, first strand: chain 'H' and resid 287 through 288 removed outlier: 3.537A pdb=" N GLU H 280 " --> pdb=" O ASN H 288 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG H 268 " --> pdb=" O GLU H 276 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 278 " --> pdb=" O TRP H 266 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP H 266 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 326 " --> pdb=" O SER H 265 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.048A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.509A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 233 through 234 Processing sheet with id=AF4, first strand: chain 'L' and resid 238 through 240 removed outlier: 5.652A pdb=" N GLN L 267 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR L 276 " --> pdb=" O GLN L 267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 238 through 240 1007 hydrogen bonds defined for protein. 2886 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: 9.47 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8260 1.34 - 1.46: 6182 1.46 - 1.58: 10923 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 25542 Sorted by residual: bond pdb=" CG PRO A 69 " pdb=" CD PRO A 69 " ideal model delta sigma weight residual 1.503 1.567 -0.064 3.40e-02 8.65e+02 3.56e+00 bond pdb=" CB PRO A 69 " pdb=" CG PRO A 69 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.04e+00 bond pdb=" C THR C 103 " pdb=" N PRO C 104 " ideal model delta sigma weight residual 1.336 1.352 -0.017 9.80e-03 1.04e+04 2.84e+00 bond pdb=" CB ASN B 432 " pdb=" CG ASN B 432 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.11e+00 bond pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.89e+00 ... (remaining 25537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 34744 2.85 - 5.69: 234 5.69 - 8.54: 16 8.54 - 11.38: 4 11.38 - 14.23: 2 Bond angle restraints: 35000 Sorted by residual: angle pdb=" C ASP D 655 " pdb=" CA ASP D 655 " pdb=" CB ASP D 655 " ideal model delta sigma weight residual 117.23 110.37 6.86 1.36e+00 5.41e-01 2.55e+01 angle pdb=" CA LEU B 89 " pdb=" CB LEU B 89 " pdb=" CG LEU B 89 " ideal model delta sigma weight residual 116.30 130.53 -14.23 3.50e+00 8.16e-02 1.65e+01 angle pdb=" N SER H 63 " pdb=" CA SER H 63 " pdb=" C SER H 63 " ideal model delta sigma weight residual 114.56 109.45 5.11 1.27e+00 6.20e-01 1.62e+01 angle pdb=" CA ASP D 655 " pdb=" C ASP D 655 " pdb=" N TYR D 656 " ideal model delta sigma weight residual 119.98 116.69 3.29 8.50e-01 1.38e+00 1.50e+01 angle pdb=" CA PRO A 69 " pdb=" N PRO A 69 " pdb=" CD PRO A 69 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 ... (remaining 34995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13065 17.98 - 35.97: 1385 35.97 - 53.95: 399 53.95 - 71.93: 54 71.93 - 89.92: 18 Dihedral angle restraints: 14921 sinusoidal: 4567 harmonic: 10354 Sorted by residual: dihedral pdb=" CB CYS A 725 " pdb=" SG CYS A 725 " pdb=" SG CYS A 779 " pdb=" CB CYS A 779 " ideal model delta sinusoidal sigma weight residual -86.00 -168.77 82.77 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS H 251 " pdb=" SG CYS H 251 " pdb=" SG CYS H 325 " pdb=" CB CYS H 325 " ideal model delta sinusoidal sigma weight residual 93.00 175.26 -82.26 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 173.75 -80.75 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 14918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3100 0.044 - 0.088: 786 0.088 - 0.133: 234 0.133 - 0.177: 13 0.177 - 0.221: 1 Chirality restraints: 4134 Sorted by residual: chirality pdb=" CB THR A 664 " pdb=" CA THR A 664 " pdb=" OG1 THR A 664 " pdb=" CG2 THR A 664 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA THR C 105 " pdb=" N THR C 105 " pdb=" C THR C 105 " pdb=" CB THR C 105 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB ILE A 513 " pdb=" CA ILE A 513 " pdb=" CG1 ILE A 513 " pdb=" CG2 ILE A 513 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 4131 not shown) Planarity restraints: 4523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 106 " -0.018 2.00e-02 2.50e+03 1.57e-02 6.13e+00 pdb=" CG TRP H 106 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP H 106 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP H 106 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 106 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 106 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 106 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 106 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 106 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 79 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C CYS A 79 " 0.040 2.00e-02 2.50e+03 pdb=" O CYS A 79 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 68 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 69 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.032 5.00e-02 4.00e+02 ... (remaining 4520 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 661 2.69 - 3.24: 24465 3.24 - 3.80: 36887 3.80 - 4.35: 42106 4.35 - 4.90: 72794 Nonbonded interactions: 176913 Sorted by model distance: nonbonded pdb=" O PHE B 660 " pdb=" OH TYR B 684 " model vdw 2.140 3.040 nonbonded pdb=" O LEU C 325 " pdb=" OG SER C 328 " model vdw 2.185 3.040 nonbonded pdb=" O SER H 314 " pdb=" OG SER H 314 " model vdw 2.219 3.040 nonbonded pdb=" N GLU B 271 " pdb=" OE1 GLU B 271 " model vdw 2.240 3.120 nonbonded pdb=" NE1 TRP A 381 " pdb=" O GLU A 387 " model vdw 2.246 3.120 ... (remaining 176908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 or (resid 39 through 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 46 or (resid 47 and ( \ name N or name CA or name C or name O or name CB )) or resid 48 through 51 or (r \ esid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 or \ resid 55 through 57 or (resid 58 through 60 and (name N or name CA or name C or \ name O or name CB )) or resid 61 through 80 or (resid 81 through 82 and (name N \ or name CA or name C or name O or name CB )) or resid 83 through 98 or (resid 99 \ through 100 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 01 or (resid 102 through 103 and (name N or name CA or name C or name O or name \ CB )) or resid 104 through 121 or (resid 122 and (name N or name CA or name C or \ name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 152 or (resid 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 155 or (resid 156 \ and (name N or name CA or name C or name O or name CB )) or resid 157 through 1 \ 85 or (resid 186 and (name N or name CA or name C or name O or name CB )) or res \ id 187 through 189 or (resid 190 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 208 or (resid 209 through 211 and (na \ me N or name CA or name C or name O or name CB )) or resid 212 through 214 or (r \ esid 215 through 217 and (name N or name CA or name C or name O or name CB )) or \ resid 218 through 224 or (resid 225 and (name N or name CA or name C or name O \ or name CB )) or resid 226 or (resid 227 through 229 and (name N or name CA or n \ ame C or name O or name CB )) or resid 230 through 232 or (resid 233 through 236 \ and (name N or name CA or name C or name O or name CB )) or resid 237 through 2 \ 48 or (resid 249 and (name N or name CA or name C or name O or name CB )) or res \ id 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) or \ resid 252 through 259 or (resid 260 and (name N or name CA or name C or name O \ or name CB )) or resid 261 through 271 or (resid 272 through 273 and (name N or \ name CA or name C or name O or name CB )) or resid 274 or (resid 275 and (name N \ or name CA or name C or name O or name CB )) or resid 276 through 282 or (resid \ 283 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 326 or (resid 327 and (name N or name CA or name C or name O or n \ ame CB )) or resid 328 through 329 or (resid 330 through 332 and (name N or name \ CA or name C or name O or name CB )) or resid 333 through 338 or (resid 339 and \ (name N or name CA or name C or name O or name CB )) or resid 340 through 346 o \ r (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 48 through 353 or (resid 354 and (name N or name CA or name C or name O or name \ CB )) or resid 355 through 357 or resid 359 or (resid 360 and (name N or name CA \ or name C or name O or name CB )) or resid 361 through 370 or (resid 371 and (n \ ame N or name CA or name C or name O or name CB )) or resid 372 through 375 or ( \ resid 376 and (name N or name CA or name C or name O or name CB )) or resid 377 \ through 384 or (resid 385 and (name N or name CA or name C or name O or name CB \ )) or resid 386 or (resid 387 and (name N or name CA or name C or name O or name \ CB )) or resid 388 through 393 or (resid 394 and (name N or name CA or name C o \ r name O or name CB )) or resid 395 through 398 or (resid 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 415 or (resid 416 th \ rough 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB )) or resid \ 420 or (resid 421 through 424 and (name N or name CA or name C or name O or name \ CB )) or resid 425 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 or (resid 429 and (name N or name CA or name \ C or name O or name CB )) or resid 430 through 445 or (resid 446 and (name N or \ name CA or name C or name O or name CB )) or resid 447 through 450 or (resid 45 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 452 through \ 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) or re \ sid 471 through 488 or (resid 489 and (name N or name CA or name C or name O or \ name CB )) or resid 490 or (resid 491 through 492 and (name N or name CA or name \ C or name O or name CB )) or resid 493 or (resid 494 and (name N or name CA or \ name C or name O or name CB )) or resid 495 through 510 or (resid 511 and (name \ N or name CA or name C or name O or name CB )) or resid 512 through 542 or (resi \ d 543 through 546 and (name N or name CA or name C or name O or name CB )) or re \ sid 547 through 550 or (resid 551 through 556 and (name N or name CA or name C o \ r name O or name CB )) or resid 557 through 572 or (resid 573 through 577 and (n \ ame N or name CA or name C or name O or name CB )) or resid 578 or (resid 579 th \ rough 582 and (name N or name CA or name C or name O or name CB )) or resid 583 \ or (resid 584 through 588 and (name N or name CA or name C or name O or name CB \ )) or resid 589 through 606 or (resid 607 through 613 and (name N or name CA or \ name C or name O or name CB )) or resid 614 through 634 or (resid 635 through 64 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 641 through \ 642 or (resid 643 and (name N or name CA or name C or name O or name CB )) or re \ sid 644 or (resid 645 and (name N or name CA or name C or name O or name CB )) o \ r resid 646 through 650 or (resid 651 and (name N or name CA or name C or name O \ or name CB )) or resid 652 or (resid 653 through 655 and (name N or name CA or \ name C or name O or name CB )) or resid 656 or (resid 657 through 659 and (name \ N or name CA or name C or name O or name CB )) or resid 660 through 663 or (resi \ d 664 through 667 and (name N or name CA or name C or name O or name CB )) or re \ sid 668 through 675 or (resid 676 and (name N or name CA or name C or name O or \ name CB )) or resid 677 through 679 or (resid 680 and (name N or name CA or name \ C or name O or name CB )) or resid 681 through 684 or (resid 685 and (name N or \ name CA or name C or name O or name CB )) or resid 686 or (resid 687 through 68 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 689 through \ 692 or (resid 693 and (name N or name CA or name C or name O or name CB )) or re \ sid 694 through 696 or (resid 697 through 698 and (name N or name CA or name C o \ r name O or name CB )) or resid 699 through 703 or (resid 704 and (name N or nam \ e CA or name C or name O or name CB )) or resid 705 through 723 or (resid 724 an \ d (name N or name CA or name C or name O or name CB )) or resid 725 through 731 \ or (resid 732 and (name N or name CA or name C or name O or name CB )) or resid \ 733 through 744 or (resid 745 through 746 and (name N or name CA or name C or na \ me O or name CB )) or resid 747 through 750 or (resid 751 and (name N or name CA \ or name C or name O or name CB )) or resid 752 through 761 or (resid 762 and (n \ ame N or name CA or name C or name O or name CB )) or resid 763 through 769 or ( \ resid 770 through 771 and (name N or name CA or name C or name O or name CB )) o \ r resid 772 through 775 or (resid 776 through 778 and (name N or name CA or name \ C or name O or name CB )) or resid 779 through 789 or (resid 790 through 793 an \ d (name N or name CA or name C or name O or name CB )) or (resid 794 through 801 \ and (name N or name CA or name C or name O or name CB )) or resid 802 or (resid \ 803 through 813 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 27 through 49 or (resid 50 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 or resid 55 through 169 or (res \ id 170 and (name N or name CA or name C or name O or name CB )) or resid 171 thr \ ough 184 or (resid 185 through 186 and (name N or name CA or name C or name O or \ name CB )) or resid 187 through 263 or (resid 264 and (name N or name CA or nam \ e C or name O or name CB )) or resid 265 through 292 or (resid 293 and (name N o \ r name CA or name C or name O or name CB )) or resid 294 through 296 or (resid 2 \ 97 through 300 and (name N or name CA or name C or name O or name CB )) or resid \ 301 through 303 or (resid 304 and (name N or name CA or name C or name O or nam \ e CB )) or resid 305 through 310 or (resid 311 and (name N or name CA or name C \ or name O or name CB )) or resid 312 through 357 or resid 359 through 411 or (re \ sid 412 and (name N or name CA or name C or name O or name CB )) or resid 413 th \ rough 447 or (resid 448 through 449 and (name N or name CA or name C or name O o \ r name CB )) or resid 450 through 482 or (resid 483 and (name N or name CA or na \ me C or name O or name CB )) or resid 484 through 485 or (resid 486 and (name N \ or name CA or name C or name O or name CB )) or resid 487 through 501 or (resid \ 502 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 561 or (resid 562 and (name N or name CA or name C or name O or name CB )) or \ resid 563 through 565 or (resid 566 and (name N or name CA or name C or name O o \ r name CB )) or resid 567 or (resid 568 through 569 and (name N or name CA or na \ me C or name O or name CB )) or resid 570 through 584 or (resid 585 through 588 \ and (name N or name CA or name C or name O or name CB )) or resid 589 through 59 \ 1 or (resid 592 and (name N or name CA or name C or name O or name CB )) or resi \ d 593 through 611 or (resid 612 through 613 and (name N or name CA or name C or \ name O or name CB )) or resid 614 through 619 or (resid 620 through 624 and (nam \ e N or name CA or name C or name O or name CB )) or resid 625 through 677 or (re \ sid 678 through 680 and (name N or name CA or name C or name O or name CB )) or \ resid 681 through 690 or (resid 691 and (name N or name CA or name C or name O o \ r name CB )) or resid 692 through 726 or (resid 727 and (name N or name CA or na \ me C or name O or name CB )) or resid 728 through 766 or (resid 767 and (name N \ or name CA or name C or name O or name CB )) or resid 768 through 774 or (resid \ 775 through 778 and (name N or name CA or name C or name O or name CB )) or resi \ d 779 through 784 or (resid 785 through 786 and (name N or name CA or name C or \ name O or name CB )) or resid 787 through 813)) } ncs_group { reference = (chain 'B' and (resid 35 through 41 or (resid 42 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 76 or (resid 77 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 89 or (resid 90 through 91 and (name N or name CA or name C or name O or name \ CB )) or (resid 92 through 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 97 through 101 or (resid 102 through 108 and (name N or name CA \ or name C or name O or name CB )) or resid 109 through 113 or (resid 114 and (n \ ame N or name CA or name C or name O or name CB )) or resid 115 through 149 or ( \ resid 150 and (name N or name CA or name C or name O or name CB )) or resid 151 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 208 or (resid 209 and (name N or name CA or name C or na \ me O or name CB )) or resid 210 or (resid 211 and (name N or name CA or name C o \ r name O or name CB )) or resid 212 through 231 or (resid 232 and (name N or nam \ e CA or name C or name O or name CB )) or resid 233 through 281 or (resid 282 th \ rough 283 and (name N or name CA or name C or name O or name CB )) or resid 284 \ or (resid 285 and (name N or name CA or name C or name O or name CB )) or resid \ 286 or (resid 287 and (name N or name CA or name C or name O or name CB )) or re \ sid 288 through 303 or (resid 304 through 306 and (name N or name CA or name C o \ r name O or name CB )) or resid 307 through 309 or (resid 310 through 312 and (n \ ame N or name CA or name C or name O or name CB )) or resid 313 through 316 or ( \ resid 317 through 319 and (name N or name CA or name C or name O or name CB )) o \ r resid 320 through 330 or (resid 331 through 333 and (name N or name CA or name \ C or name O or name CB )) or resid 334 through 343 or (resid 344 and (name N or \ name CA or name C or name O or name CB )) or resid 345 or (resid 346 and (name \ N or name CA or name C or name O or name CB )) or resid 347 through 367 or (resi \ d 368 through 369 and (name N or name CA or name C or name O or name CB )) or re \ sid 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) o \ r resid 372 through 381 or (resid 382 and (name N or name CA or name C or name O \ or name CB )) or resid 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB )) or resid 385 through 388 or (resid 389 and (name N or name CA \ or name C or name O or name CB )) or resid 390 through 393 or (resid 394 throug \ h 395 and (name N or name CA or name C or name O or name CB )) or resid 396 or ( \ resid 397 through 400 and (name N or name CA or name C or name O or name CB )) o \ r resid 401 through 402 or (resid 403 and (name N or name CA or name C or name O \ or name CB )) or resid 404 through 419 or (resid 420 through 421 and (name N or \ name CA or name C or name O or name CB )) or resid 422 or (resid 423 and (name \ N or name CA or name C or name O or name CB )) or resid 424 or (resid 425 and (n \ ame N or name CA or name C or name O or name CB )) or resid 426 or (resid 427 th \ rough 428 and (name N or name CA or name C or name O or name CB )) or resid 429 \ through 437 or (resid 438 and (name N or name CA or name C or name O or name CB \ )) or resid 439 or (resid 440 through 448 and (name N or name CA or name C or na \ me O or name CB )) or resid 449 through 471 or (resid 472 and (name N or name CA \ or name C or name O or name CB )) or resid 473 or (resid 474 and (name N or nam \ e CA or name C or name O or name CB )) or resid 475 through 480 or (resid 481 th \ rough 482 and (name N or name CA or name C or name O or name CB )) or resid 483 \ or (resid 484 and (name N or name CA or name C or name O or name CB )) or resid \ 485 through 493 or (resid 494 and (name N or name CA or name C or name O or name \ CB )) or resid 495 through 510 or (resid 511 and (name N or name CA or name C o \ r name O or name CB )) or resid 512 through 522 or (resid 523 and (name N or nam \ e CA or name C or name O or name CB )) or resid 524 or (resid 525 and (name N or \ name CA or name C or name O or name CB )) or resid 526 through 535 or (resid 53 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 537 or (resi \ d 538 and (name N or name CA or name C or name O or name CB )) or resid 539 thro \ ugh 540 or (resid 541 and (name N or name CA or name C or name O or name CB )) o \ r resid 542 through 590 or (resid 591 through 593 and (name N or name CA or name \ C or name O or name CB )) or resid 594 through 606 or (resid 607 through 609 an \ d (name N or name CA or name C or name O or name CB )) or resid 610 through 618 \ or (resid 619 through 621 and (name N or name CA or name C or name O or name CB \ )) or resid 622 through 627 or (resid 628 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 640 or (resid 641 through 64 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 644 through \ 646 or (resid 647 and (name N or name CA or name C or name O or name CB )) or re \ sid 648 through 663 or (resid 664 through 665 and (name N or name CA or name C o \ r name O or name CB )) or resid 666 through 669 or (resid 670 and (name N or nam \ e CA or name C or name O or name CB )) or resid 671 through 676 or (resid 677 an \ d (name N or name CA or name C or name O or name CB )) or resid 678 through 682 \ or (resid 683 and (name N or name CA or name C or name O or name CB )) or resid \ 684 through 685 or (resid 686 through 687 and (name N or name CA or name C or na \ me O or name CB )) or resid 688 or (resid 689 and (name N or name CA or name C o \ r name O or name CB )) or resid 690 through 696 or (resid 697 through 698 and (n \ ame N or name CA or name C or name O or name CB )) or resid 699 through 700 or ( \ resid 701 through 702 and (name N or name CA or name C or name O or name CB )) o \ r (resid 703 through 707 and (name N or name CA or name C or name O or name CB ) \ ) or resid 708 through 720 or (resid 721 through 723 and (name N or name CA or n \ ame C or name O or name CB )) or resid 724 through 733 or (resid 734 through 737 \ and (name N or name CA or name C or name O or name CB )) or resid 738 through 7 \ 66 or (resid 767 and (name N or name CA or name C or name O or name CB )) or res \ id 768 through 780 or (resid 781 through 791 and (name N or name CA or name C or \ name O or name CB )) or resid 792 through 793 or (resid 794 through 814 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 35 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 64 or (resid 65 through 66 and (na \ me N or name CA or name C or name O or name CB )) or resid 67 through 136 or (re \ sid 137 and (name N or name CA or name C or name O or name CB )) or resid 138 th \ rough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 198 or (resid 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 241 or (resid 242 through 243 and (name N \ or name CA or name C or name O or name CB )) or resid 244 through 311 or (resid \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throug \ h 325 or (resid 326 and (name N or name CA or name C or name O or name CB )) or \ resid 327 through 399 or (resid 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 411 or (resid 412 through 414 and (name N or n \ ame CA or name C or name O or name CB )) or resid 415 through 519 or (resid 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 55 \ 3 or (resid 554 through 557 and (name N or name CA or name C or name O or name C \ B )) or resid 558 through 563 or (resid 564 and (name N or name CA or name C or \ name O or name CB )) or resid 565 through 566 or (resid 567 and (name N or name \ CA or name C or name O or name CB )) or resid 568 through 575 or (resid 576 thro \ ugh 579 and (name N or name CA or name C or name O or name CB )) or resid 580 or \ (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 2 through 591 or (resid 592 through 593 and (name N or name CA or name C or name \ O or name CB )) or resid 594 through 619 or (resid 620 through 621 and (name N \ or name CA or name C or name O or name CB )) or resid 622 through 641 or (resid \ 642 through 643 and (name N or name CA or name C or name O or name CB )) or resi \ d 644 through 655 or (resid 656 through 657 and (name N or name CA or name C or \ name O or name CB )) or resid 658 through 694 or (resid 695 through 698 and (nam \ e N or name CA or name C or name O or name CB )) or resid 699 through 746 or (re \ sid 747 and (name N or name CA or name C or name O or name CB )) or resid 748 th \ rough 752 or (resid 753 and (name N or name CA or name C or name O or name CB )) \ or resid 754 through 768 or (resid 769 through 770 and (name N or name CA or na \ me C or name O or name CB )) or resid 771 through 773 or (resid 774 and (name N \ or name CA or name C or name O or name CB )) or resid 775 through 778 or (resid \ 779 and (name N or name CA or name C or name O or name CB )) or resid 780 throug \ h 794 or (resid 795 through 814 and (name N or name CA or name C or name O or na \ me CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 1.160 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 61.220 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.100 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25562 Z= 0.124 Angle : 0.606 14.230 35040 Z= 0.313 Chirality : 0.042 0.221 4134 Planarity : 0.004 0.058 4523 Dihedral : 16.374 89.915 8181 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.56 % Favored : 88.02 % Rotamer: Outliers : 0.42 % Allowed : 36.62 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3555 helix: 2.06 (0.16), residues: 1184 sheet: -1.96 (0.23), residues: 526 loop : -2.61 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP H 106 HIS 0.006 0.001 HIS B 96 PHE 0.026 0.001 PHE D 115 TYR 0.019 0.001 TYR L 50 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.16793 ( 995) hydrogen bonds : angle 5.85086 ( 2886) SS BOND : bond 0.00199 ( 20) SS BOND : angle 1.70532 ( 40) covalent geometry : bond 0.00283 (25542) covalent geometry : angle 0.60332 (35000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 256 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 MET cc_start: 0.3934 (ptt) cc_final: 0.2482 (mmp) outliers start: 9 outliers final: 4 residues processed: 263 average time/residue: 0.3018 time to fit residues: 136.6239 Evaluate side-chains 251 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 768 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 8.9990 chunk 269 optimal weight: 0.0670 chunk 149 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 323 optimal weight: 40.0000 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.158919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109953 restraints weight = 48783.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106555 restraints weight = 38600.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106362 restraints weight = 34827.141| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25562 Z= 0.237 Angle : 0.666 9.678 35040 Z= 0.347 Chirality : 0.045 0.224 4134 Planarity : 0.004 0.052 4523 Dihedral : 4.699 51.476 3777 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.25 % Favored : 86.30 % Rotamer: Outliers : 7.16 % Allowed : 32.04 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3555 helix: 2.12 (0.15), residues: 1208 sheet: -2.15 (0.21), residues: 579 loop : -2.65 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 378 HIS 0.009 0.001 HIS C 477 PHE 0.025 0.002 PHE A 533 TYR 0.013 0.002 TYR A 684 ARG 0.005 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 995) hydrogen bonds : angle 4.67847 ( 2886) SS BOND : bond 0.00316 ( 20) SS BOND : angle 1.78161 ( 40) covalent geometry : bond 0.00573 (25542) covalent geometry : angle 0.66413 (35000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 243 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7984 (pp30) REVERT: A 761 HIS cc_start: 0.8901 (OUTLIER) cc_final: 0.8609 (t70) REVERT: B 159 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9066 (mp) REVERT: B 251 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8961 (t80) REVERT: B 561 MET cc_start: 0.3543 (ptt) cc_final: 0.2625 (mmp) REVERT: C 478 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8884 (tt) REVERT: C 648 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 387 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7408 (m90) REVERT: D 406 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8378 (pp) outliers start: 153 outliers final: 86 residues processed: 374 average time/residue: 0.3025 time to fit residues: 195.1433 Evaluate side-chains 331 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 237 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain H residue 325 CYS Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 332 optimal weight: 50.0000 chunk 164 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 40.0000 chunk 61 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN C 73 GLN D 68 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.168013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123354 restraints weight = 49924.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118164 restraints weight = 41224.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118484 restraints weight = 38948.235| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25562 Z= 0.104 Angle : 0.570 10.418 35040 Z= 0.292 Chirality : 0.042 0.226 4134 Planarity : 0.003 0.050 4523 Dihedral : 4.392 52.611 3774 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.52 % Favored : 89.03 % Rotamer: Outliers : 6.36 % Allowed : 32.46 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3555 helix: 2.22 (0.15), residues: 1230 sheet: -1.70 (0.23), residues: 523 loop : -2.65 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 106 HIS 0.003 0.000 HIS H 54 PHE 0.015 0.001 PHE B 310 TYR 0.016 0.001 TYR A 776 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 995) hydrogen bonds : angle 4.14227 ( 2886) SS BOND : bond 0.00246 ( 20) SS BOND : angle 1.41668 ( 40) covalent geometry : bond 0.00237 (25542) covalent geometry : angle 0.56784 (35000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 266 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8793 (mp) cc_final: 0.8462 (mp) REVERT: B 44 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.5993 (t-90) REVERT: B 159 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8620 (mp) REVERT: B 259 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8642 (p) REVERT: B 561 MET cc_start: 0.3609 (ptt) cc_final: 0.2615 (mmp) REVERT: C 478 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8831 (tt) REVERT: D 387 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7316 (m90) REVERT: D 406 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8235 (pp) REVERT: H 106 TRP cc_start: 0.7945 (t60) cc_final: 0.7593 (t60) outliers start: 136 outliers final: 84 residues processed: 381 average time/residue: 0.3012 time to fit residues: 194.0433 Evaluate side-chains 340 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 250 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 220 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 345 optimal weight: 0.9980 chunk 136 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 130 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 260 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN C 357 GLN C 597 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.169020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3668 r_free = 0.3668 target = 0.126023 restraints weight = 50460.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119714 restraints weight = 49307.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120817 restraints weight = 44471.304| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25562 Z= 0.102 Angle : 0.552 9.325 35040 Z= 0.282 Chirality : 0.042 0.204 4134 Planarity : 0.003 0.050 4523 Dihedral : 4.243 53.092 3774 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.91 % Favored : 88.64 % Rotamer: Outliers : 7.02 % Allowed : 31.20 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3555 helix: 2.28 (0.15), residues: 1229 sheet: -1.71 (0.23), residues: 534 loop : -2.58 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 378 HIS 0.003 0.000 HIS C 477 PHE 0.037 0.001 PHE B 310 TYR 0.011 0.001 TYR L 50 ARG 0.004 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 995) hydrogen bonds : angle 3.95562 ( 2886) SS BOND : bond 0.00218 ( 20) SS BOND : angle 1.15166 ( 40) covalent geometry : bond 0.00235 (25542) covalent geometry : angle 0.55099 (35000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 269 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 HIS cc_start: 0.7429 (t70) cc_final: 0.7227 (t-170) REVERT: A 82 LEU cc_start: 0.8774 (mp) cc_final: 0.8478 (mp) REVERT: A 761 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8666 (t70) REVERT: B 44 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6089 (t-90) REVERT: B 153 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: B 159 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8966 (mp) REVERT: B 259 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8728 (p) REVERT: B 561 MET cc_start: 0.3517 (ptt) cc_final: 0.2406 (mmp) REVERT: C 478 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8812 (tt) REVERT: D 73 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8759 (mp) REVERT: D 112 MET cc_start: 0.8652 (tpp) cc_final: 0.8419 (tpp) REVERT: D 218 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7241 (mt0) REVERT: D 387 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7343 (m90) REVERT: D 406 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8223 (pp) outliers start: 150 outliers final: 102 residues processed: 398 average time/residue: 0.3079 time to fit residues: 209.1625 Evaluate side-chains 367 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 255 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 674 PHE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 743 ILE Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 302 optimal weight: 2.9990 chunk 349 optimal weight: 40.0000 chunk 338 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 135 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.165306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121598 restraints weight = 49884.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116396 restraints weight = 42067.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116726 restraints weight = 39978.739| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25562 Z= 0.116 Angle : 0.563 9.718 35040 Z= 0.287 Chirality : 0.042 0.200 4134 Planarity : 0.003 0.050 4523 Dihedral : 4.256 53.602 3774 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.20 % Favored : 88.35 % Rotamer: Outliers : 7.11 % Allowed : 31.10 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3555 helix: 2.34 (0.15), residues: 1230 sheet: -1.63 (0.24), residues: 517 loop : -2.56 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP H 106 HIS 0.004 0.001 HIS C 477 PHE 0.039 0.001 PHE B 310 TYR 0.024 0.001 TYR L 50 ARG 0.004 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 995) hydrogen bonds : angle 3.88248 ( 2886) SS BOND : bond 0.00188 ( 20) SS BOND : angle 1.39791 ( 40) covalent geometry : bond 0.00277 (25542) covalent geometry : angle 0.56174 (35000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 261 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 HIS cc_start: 0.7411 (t70) cc_final: 0.7185 (t-170) REVERT: A 761 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8705 (t70) REVERT: B 44 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6091 (t-90) REVERT: B 153 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: B 159 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8809 (mp) REVERT: B 259 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 561 MET cc_start: 0.3494 (ptt) cc_final: 0.2461 (mmp) REVERT: C 158 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: C 478 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8796 (tt) REVERT: C 648 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7666 (tp) REVERT: D 73 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (mp) REVERT: D 112 MET cc_start: 0.8680 (tpp) cc_final: 0.8418 (tpp) REVERT: D 143 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8386 (m) REVERT: D 153 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: D 387 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7346 (m90) REVERT: D 406 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8267 (pp) outliers start: 152 outliers final: 114 residues processed: 391 average time/residue: 0.2924 time to fit residues: 194.7206 Evaluate side-chains 381 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 254 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 743 ILE Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 143 optimal weight: 0.0020 chunk 235 optimal weight: 50.0000 chunk 64 optimal weight: 0.6980 chunk 326 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.165703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124503 restraints weight = 49660.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118259 restraints weight = 49935.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119609 restraints weight = 47499.328| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25562 Z= 0.113 Angle : 0.563 10.086 35040 Z= 0.285 Chirality : 0.042 0.222 4134 Planarity : 0.003 0.050 4523 Dihedral : 4.216 54.193 3774 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.03 % Favored : 88.55 % Rotamer: Outliers : 7.44 % Allowed : 30.96 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3555 helix: 2.38 (0.15), residues: 1229 sheet: -1.60 (0.24), residues: 517 loop : -2.53 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 378 HIS 0.004 0.001 HIS C 477 PHE 0.041 0.001 PHE B 310 TYR 0.010 0.001 TYR H 60 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 995) hydrogen bonds : angle 3.81175 ( 2886) SS BOND : bond 0.00209 ( 20) SS BOND : angle 1.30878 ( 40) covalent geometry : bond 0.00268 (25542) covalent geometry : angle 0.56115 (35000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 264 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 HIS cc_start: 0.7294 (t70) cc_final: 0.7052 (t-170) REVERT: A 315 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7748 (t60) REVERT: A 526 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7472 (p90) REVERT: A 654 ARG cc_start: 0.8922 (mtp-110) cc_final: 0.8556 (mmm160) REVERT: A 761 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8592 (t70) REVERT: B 44 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.6069 (t-90) REVERT: B 146 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.8877 (mm-40) REVERT: B 153 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: B 159 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 259 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 561 MET cc_start: 0.3425 (ptt) cc_final: 0.2306 (mmp) REVERT: C 158 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: C 478 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (tt) REVERT: C 648 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7664 (tp) REVERT: C 743 MET cc_start: 0.8446 (mmm) cc_final: 0.8210 (mmm) REVERT: D 73 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8639 (mp) REVERT: D 112 MET cc_start: 0.8603 (tpp) cc_final: 0.8364 (tpp) REVERT: D 143 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8356 (m) REVERT: D 218 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7219 (mt0) REVERT: D 387 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7355 (m90) REVERT: D 406 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8239 (pp) outliers start: 159 outliers final: 121 residues processed: 400 average time/residue: 0.3013 time to fit residues: 204.4004 Evaluate side-chains 389 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 252 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 743 ILE Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 325 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 187 optimal weight: 0.1980 chunk 106 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 338 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.170980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131282 restraints weight = 50299.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123888 restraints weight = 47626.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125066 restraints weight = 48929.512| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25562 Z= 0.099 Angle : 0.555 10.446 35040 Z= 0.281 Chirality : 0.042 0.228 4134 Planarity : 0.003 0.051 4523 Dihedral : 4.130 54.117 3774 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.41 % Favored : 89.20 % Rotamer: Outliers : 6.92 % Allowed : 31.62 % Favored : 61.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3555 helix: 2.42 (0.15), residues: 1230 sheet: -1.53 (0.24), residues: 518 loop : -2.54 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 106 HIS 0.003 0.000 HIS H 54 PHE 0.044 0.001 PHE B 310 TYR 0.019 0.001 TYR A 776 ARG 0.005 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.02647 ( 995) hydrogen bonds : angle 3.72311 ( 2886) SS BOND : bond 0.00181 ( 20) SS BOND : angle 1.18268 ( 40) covalent geometry : bond 0.00228 (25542) covalent geometry : angle 0.55434 (35000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 268 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 HIS cc_start: 0.7382 (t70) cc_final: 0.7138 (t-170) REVERT: A 654 ARG cc_start: 0.8929 (mtp-110) cc_final: 0.8545 (mmm160) REVERT: A 761 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8634 (t70) REVERT: B 44 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6191 (t-90) REVERT: B 146 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8806 (mm-40) REVERT: B 153 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: B 159 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 259 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 561 MET cc_start: 0.3421 (ptt) cc_final: 0.2337 (mmp) REVERT: C 158 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: C 478 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8766 (tt) REVERT: C 648 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7675 (tp) REVERT: D 73 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 112 MET cc_start: 0.8615 (tpp) cc_final: 0.8370 (tpp) REVERT: D 143 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8370 (m) REVERT: D 218 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: D 406 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8235 (pp) outliers start: 148 outliers final: 117 residues processed: 395 average time/residue: 0.3005 time to fit residues: 203.0990 Evaluate side-chains 386 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 256 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 236 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 127 optimal weight: 0.3980 chunk 281 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 HIS A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.164457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121115 restraints weight = 49757.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114155 restraints weight = 45754.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114920 restraints weight = 45448.682| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25562 Z= 0.174 Angle : 0.618 10.799 35040 Z= 0.314 Chirality : 0.044 0.259 4134 Planarity : 0.004 0.051 4523 Dihedral : 4.353 55.252 3774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.98 % Favored : 87.62 % Rotamer: Outliers : 7.62 % Allowed : 31.06 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3555 helix: 2.40 (0.15), residues: 1228 sheet: -1.67 (0.23), residues: 527 loop : -2.54 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 106 HIS 0.007 0.001 HIS C 477 PHE 0.043 0.001 PHE B 310 TYR 0.016 0.001 TYR L 50 ARG 0.004 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 995) hydrogen bonds : angle 3.89399 ( 2886) SS BOND : bond 0.00403 ( 20) SS BOND : angle 1.53910 ( 40) covalent geometry : bond 0.00418 (25542) covalent geometry : angle 0.61599 (35000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 250 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.8286 (OUTLIER) cc_final: 0.7612 (t60) REVERT: A 526 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7627 (p90) REVERT: A 761 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8645 (t70) REVERT: B 44 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6140 (t-90) REVERT: B 112 MET cc_start: 0.9016 (mmm) cc_final: 0.8690 (mmm) REVERT: B 153 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: B 246 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8960 (mp) REVERT: B 561 MET cc_start: 0.3345 (ptt) cc_final: 0.2368 (mmp) REVERT: C 158 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: C 478 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8775 (tt) REVERT: C 648 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7628 (tp) REVERT: D 87 CYS cc_start: 0.4881 (m) cc_final: 0.4547 (m) REVERT: D 115 PHE cc_start: 0.9166 (t80) cc_final: 0.8908 (t80) REVERT: D 143 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8394 (m) REVERT: D 387 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7403 (m90) REVERT: D 406 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8376 (pp) outliers start: 163 outliers final: 125 residues processed: 391 average time/residue: 0.2908 time to fit residues: 195.5271 Evaluate side-chains 384 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 247 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 79 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 346 optimal weight: 0.0060 chunk 312 optimal weight: 40.0000 chunk 11 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 205 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.166909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126578 restraints weight = 49712.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120582 restraints weight = 49079.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121589 restraints weight = 47271.905| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25562 Z= 0.100 Angle : 0.570 11.101 35040 Z= 0.287 Chirality : 0.042 0.270 4134 Planarity : 0.003 0.051 4523 Dihedral : 4.194 55.411 3774 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.10 % Favored : 89.54 % Rotamer: Outliers : 5.85 % Allowed : 33.30 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3555 helix: 2.47 (0.15), residues: 1223 sheet: -1.54 (0.23), residues: 527 loop : -2.52 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP H 106 HIS 0.003 0.000 HIS H 54 PHE 0.046 0.001 PHE B 310 TYR 0.021 0.001 TYR L 50 ARG 0.004 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.02592 ( 995) hydrogen bonds : angle 3.68755 ( 2886) SS BOND : bond 0.00184 ( 20) SS BOND : angle 1.36872 ( 40) covalent geometry : bond 0.00229 (25542) covalent geometry : angle 0.56871 (35000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 266 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8093 (mmm) cc_final: 0.7893 (mmt) REVERT: A 526 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7481 (p90) REVERT: A 654 ARG cc_start: 0.8866 (mtp-110) cc_final: 0.8510 (mmm160) REVERT: A 761 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8594 (t70) REVERT: B 44 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.6086 (t-90) REVERT: B 112 MET cc_start: 0.8977 (mmm) cc_final: 0.8599 (mmm) REVERT: B 153 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8364 (mt0) REVERT: B 246 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8920 (mp) REVERT: B 561 MET cc_start: 0.3415 (ptt) cc_final: 0.2240 (mmp) REVERT: C 158 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: C 478 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8722 (tt) REVERT: C 648 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7660 (tp) REVERT: D 87 CYS cc_start: 0.4397 (m) cc_final: 0.4038 (m) REVERT: D 112 MET cc_start: 0.8610 (tpp) cc_final: 0.8363 (tpp) REVERT: D 115 PHE cc_start: 0.9075 (t80) cc_final: 0.8855 (t80) REVERT: D 143 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (m) REVERT: D 406 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8229 (pp) outliers start: 125 outliers final: 102 residues processed: 372 average time/residue: 0.2965 time to fit residues: 188.3375 Evaluate side-chains 369 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 257 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 29 optimal weight: 3.9990 chunk 164 optimal weight: 0.0040 chunk 158 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 294 optimal weight: 40.0000 chunk 209 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 322 optimal weight: 0.6980 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN D 356 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121078 restraints weight = 48503.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113169 restraints weight = 53519.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114181 restraints weight = 49787.560| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25562 Z= 0.226 Angle : 0.669 10.261 35040 Z= 0.344 Chirality : 0.045 0.293 4134 Planarity : 0.004 0.051 4523 Dihedral : 4.580 58.104 3774 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.11 % Favored : 86.55 % Rotamer: Outliers : 6.31 % Allowed : 32.97 % Favored : 60.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3555 helix: 2.33 (0.15), residues: 1226 sheet: -1.89 (0.23), residues: 536 loop : -2.57 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 151 HIS 0.009 0.001 HIS C 477 PHE 0.044 0.002 PHE B 310 TYR 0.013 0.002 TYR A 114 ARG 0.006 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 995) hydrogen bonds : angle 4.03566 ( 2886) SS BOND : bond 0.00283 ( 20) SS BOND : angle 1.66778 ( 40) covalent geometry : bond 0.00549 (25542) covalent geometry : angle 0.66728 (35000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 246 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7767 (t60) REVERT: A 526 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7729 (p90) REVERT: A 761 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8637 (t70) REVERT: B 44 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.6088 (t-90) REVERT: B 112 MET cc_start: 0.9073 (mmm) cc_final: 0.8661 (mmm) REVERT: B 246 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9029 (mp) REVERT: B 537 VAL cc_start: 0.8067 (t) cc_final: 0.7547 (m) REVERT: B 561 MET cc_start: 0.3403 (ptt) cc_final: 0.2240 (mmp) REVERT: C 158 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: C 478 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8763 (tt) REVERT: C 648 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7686 (tp) REVERT: D 87 CYS cc_start: 0.4608 (m) cc_final: 0.4210 (m) REVERT: D 112 MET cc_start: 0.8621 (tpp) cc_final: 0.8400 (tpp) REVERT: D 115 PHE cc_start: 0.9225 (t80) cc_final: 0.9010 (t80) REVERT: D 143 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8360 (m) REVERT: D 406 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8452 (pp) outliers start: 135 outliers final: 110 residues processed: 364 average time/residue: 0.2947 time to fit residues: 183.9106 Evaluate side-chains 361 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 241 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 GLN Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 266 TRP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 145 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 304 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 256 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 315 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 352 optimal weight: 50.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.165123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121278 restraints weight = 49520.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115515 restraints weight = 44226.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116311 restraints weight = 40341.288| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25562 Z= 0.125 Angle : 0.600 11.063 35040 Z= 0.303 Chirality : 0.043 0.287 4134 Planarity : 0.003 0.051 4523 Dihedral : 4.380 57.940 3774 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.52 % Favored : 89.14 % Rotamer: Outliers : 5.71 % Allowed : 33.82 % Favored : 60.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3555 helix: 2.40 (0.15), residues: 1228 sheet: -1.64 (0.23), residues: 516 loop : -2.60 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 106 HIS 0.005 0.001 HIS C 477 PHE 0.046 0.001 PHE B 310 TYR 0.011 0.001 TYR C 144 ARG 0.004 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 995) hydrogen bonds : angle 3.78828 ( 2886) SS BOND : bond 0.00197 ( 20) SS BOND : angle 1.38111 ( 40) covalent geometry : bond 0.00298 (25542) covalent geometry : angle 0.59836 (35000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8863.32 seconds wall clock time: 153 minutes 28.60 seconds (9208.60 seconds total)