Starting phenix.real_space_refine on Fri Sep 19 09:27:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vur_43537/09_2025/8vur_43537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vur_43537/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vur_43537/09_2025/8vur_43537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vur_43537/09_2025/8vur_43537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vur_43537/09_2025/8vur_43537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vur_43537/09_2025/8vur_43537.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'GLU:plan': 20, 'ASN:plan1': 8, 'ASP:plan': 9, 'HIS:plan': 4, 'ARG:plan': 10, 'PHE:plan': 6, 'TRP:plan': 1, 'TYR:plan': 1} 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: {'GLU:plan': 27, 'ARG:plan': 7, 'GLN:plan1': 7, 'ASP:plan': 19, 'ASN:plan1': 9, 'TYR:plan': 5, 'HIS:plan': 3, 'PHE:plan': 11, 'TRP:plan': 3} 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: {'GLU:plan': 33, 'GLN:plan1': 9, 'ASN:plan1': 11, 'ARG:plan': 19, 'ASP:plan': 19, 'PHE:plan': 10, 'TYR:plan': 3, 'HIS:plan': 3} 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: {'HIS:plan': 6, 'ASP:plan': 29, 'GLU:plan': 25, 'ARG:plan': 7, 'GLN:plan1': 9, 'ASN:plan1': 16, 'PHE:plan': 12, 'TYR:plan': 3, 'TRP:plan': 2} 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, 'GLU:plan': 3, 'ASP:plan': 8, 'ASN:plan1': 6, 'TYR:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'TRP: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: {'HIS:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 10, 'ARG:plan': 7, 'ASP:plan': 12, 'ASN:plan1': 6, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 202 Time building chain proxies: 6.27, per 1000 atoms: 0.25 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: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.98 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: 5.49 Time building geometry restraints manager: 3.06 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.840 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- 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 : 8.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 36 TYR 0.019 0.001 TYR L 50 PHE 0.026 0.001 PHE D 115 TRP 0.043 0.001 TRP H 106 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00283 (25542) covalent geometry : angle 0.60332 (35000) SS BOND : bond 0.00199 ( 20) SS BOND : angle 1.70532 ( 40) hydrogen bonds : bond 0.16793 ( 995) hydrogen bonds : angle 5.85086 ( 2886) *********************** 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 : 0.967 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: 0.1422 time to fit residues: 64.0560 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 : 0.968 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.158541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109831 restraints weight = 49091.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105864 restraints weight = 36758.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105694 restraints weight = 37300.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106133 restraints weight = 35182.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106220 restraints weight = 34000.142| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25562 Z= 0.239 Angle : 0.674 9.554 35040 Z= 0.351 Chirality : 0.045 0.228 4134 Planarity : 0.004 0.052 4523 Dihedral : 4.766 51.887 3777 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.61 % Favored : 85.94 % Rotamer: Outliers : 7.48 % Allowed : 31.76 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.15), residues: 3555 helix: 2.09 (0.15), residues: 1209 sheet: -2.17 (0.21), residues: 579 loop : -2.66 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 252 TYR 0.014 0.002 TYR A 684 PHE 0.026 0.002 PHE A 533 TRP 0.024 0.001 TRP B 378 HIS 0.010 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00578 (25542) covalent geometry : angle 0.67174 (35000) SS BOND : bond 0.00382 ( 20) SS BOND : angle 1.85188 ( 40) hydrogen bonds : bond 0.04553 ( 995) hydrogen bonds : angle 4.66695 ( 2886) *********************** 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 403 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 243 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8009 (pp30) REVERT: A 761 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.8738 (t70) REVERT: B 159 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9104 (mp) REVERT: B 251 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8954 (t80) REVERT: B 561 MET cc_start: 0.3551 (ptt) cc_final: 0.2715 (mmp) REVERT: C 478 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 648 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7651 (tp) REVERT: D 387 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7614 (m90) REVERT: D 406 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8388 (pp) REVERT: L 318 TYR cc_start: 0.7669 (m-10) cc_final: 0.7461 (m-10) outliers start: 160 outliers final: 94 residues processed: 380 average time/residue: 0.1359 time to fit residues: 89.0124 Evaluate side-chains 339 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 237 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 757 ILE 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 171 SER 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 319 SER 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 385 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 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 183 LEU Chi-restraints excluded: chain C residue 208 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 208 THR Chi-restraints excluded: chain D residue 222 ILE 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 743 ILE 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 98 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 153 optimal weight: 50.0000 chunk 242 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 291 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.164682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119569 restraints weight = 49655.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114371 restraints weight = 40879.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114883 restraints weight = 40064.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115331 restraints weight = 36803.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115532 restraints weight = 33023.158| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25562 Z= 0.132 Angle : 0.589 9.827 35040 Z= 0.303 Chirality : 0.043 0.223 4134 Planarity : 0.004 0.049 4523 Dihedral : 4.523 53.598 3774 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.86 % Favored : 88.69 % Rotamer: Outliers : 7.06 % Allowed : 32.18 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.15), residues: 3555 helix: 2.18 (0.15), residues: 1229 sheet: -1.85 (0.23), residues: 535 loop : -2.66 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 252 TYR 0.015 0.001 TYR A 776 PHE 0.014 0.001 PHE B 310 TRP 0.021 0.001 TRP H 264 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00310 (25542) covalent geometry : angle 0.58700 (35000) SS BOND : bond 0.00238 ( 20) SS BOND : angle 1.55293 ( 40) hydrogen bonds : bond 0.03446 ( 995) hydrogen bonds : angle 4.23017 ( 2886) *********************** 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 411 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 260 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8843 (mp) cc_final: 0.8530 (mp) REVERT: A 761 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8695 (t70) REVERT: B 44 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.5870 (t-90) REVERT: B 159 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8952 (mp) REVERT: B 251 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8988 (t80) REVERT: B 259 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 561 MET cc_start: 0.3604 (ptt) cc_final: 0.2497 (mmp) REVERT: C 478 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8845 (tt) REVERT: C 648 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7652 (tp) REVERT: C 690 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8266 (m-70) REVERT: D 406 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8286 (pp) REVERT: H 106 TRP cc_start: 0.8082 (t60) cc_final: 0.7736 (t60) REVERT: L 51 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7155 (mm-30) outliers start: 151 outliers final: 94 residues processed: 389 average time/residue: 0.1393 time to fit residues: 91.7288 Evaluate side-chains 352 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 249 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 330 TYR 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 481 ASP 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 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 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 248 LEU Chi-restraints excluded: chain B residue 251 TYR 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 409 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 THR 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 C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR 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 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 203 VAL 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 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 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 693 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 337 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 279 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 597 ASN D 119 HIS D 594 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.160370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118654 restraints weight = 49861.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110638 restraints weight = 54304.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111797 restraints weight = 54091.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112166 restraints weight = 45624.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112353 restraints weight = 40645.771| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1249 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= 0.244 Angle : 0.674 9.513 35040 Z= 0.349 Chirality : 0.045 0.254 4134 Planarity : 0.004 0.052 4523 Dihedral : 4.818 56.417 3774 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.81 % Favored : 85.74 % Rotamer: Outliers : 9.64 % Allowed : 29.93 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.15), residues: 3555 helix: 2.07 (0.15), residues: 1224 sheet: -2.15 (0.21), residues: 587 loop : -2.69 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 252 TYR 0.016 0.002 TYR B 478 PHE 0.034 0.002 PHE B 310 TRP 0.023 0.001 TRP B 378 HIS 0.009 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00590 (25542) covalent geometry : angle 0.67178 (35000) SS BOND : bond 0.00325 ( 20) SS BOND : angle 1.63992 ( 40) hydrogen bonds : bond 0.04303 ( 995) hydrogen bonds : angle 4.39065 ( 2886) *********************** 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 455 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 249 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8839 (mp) cc_final: 0.8444 (mp) REVERT: A 315 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7879 (t60) REVERT: A 761 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8676 (t70) REVERT: B 246 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9079 (mp) REVERT: B 561 MET cc_start: 0.3460 (ptt) cc_final: 0.2324 (mmp) REVERT: C 92 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9153 (m) REVERT: C 648 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7694 (tp) REVERT: D 143 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8385 (m) REVERT: D 387 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7694 (m90) REVERT: D 406 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8458 (pp) REVERT: L 51 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7434 (mm-30) outliers start: 206 outliers final: 149 residues processed: 429 average time/residue: 0.1367 time to fit residues: 101.0724 Evaluate side-chains 403 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 246 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 105 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR 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 288 VAL 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 364 VAL 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 645 ILE 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 712 TRP 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 762 GLU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 127 ILE 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 189 THR 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 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 260 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 319 SER 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 451 ASN Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 700 LEU 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 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU 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 513 ILE Chi-restraints excluded: chain C residue 517 LEU 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 757 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 157 VAL Chi-restraints excluded: chain D residue 161 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 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 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 284 TRP 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 409 VAL 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 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 688 PHE 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 58 THR 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 94 TYR 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 305 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 343 optimal weight: 0.0570 chunk 59 optimal weight: 30.0000 chunk 236 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 208 optimal weight: 0.0870 chunk 270 optimal weight: 6.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 494 ASN A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 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 = 0.4187 r_free = 0.4187 target = 0.168713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123442 restraints weight = 50005.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118443 restraints weight = 40491.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119019 restraints weight = 38335.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119741 restraints weight = 34097.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119775 restraints weight = 31973.593| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25562 Z= 0.104 Angle : 0.580 11.529 35040 Z= 0.295 Chirality : 0.042 0.196 4134 Planarity : 0.003 0.050 4523 Dihedral : 4.477 56.930 3774 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.52 % Favored : 89.03 % Rotamer: Outliers : 6.36 % Allowed : 33.49 % Favored : 60.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 3555 helix: 2.26 (0.15), residues: 1228 sheet: -1.74 (0.24), residues: 516 loop : -2.67 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 252 TYR 0.017 0.001 TYR L 50 PHE 0.029 0.001 PHE B 310 TRP 0.041 0.001 TRP H 106 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00238 (25542) covalent geometry : angle 0.57774 (35000) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.55056 ( 40) hydrogen bonds : bond 0.02864 ( 995) hydrogen bonds : angle 3.94649 ( 2886) *********************** 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 403 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 267 time to evaluate : 1.103 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 315 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.7658 (t60) REVERT: A 526 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7565 (p90) REVERT: A 761 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (t70) REVERT: B 44 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.5874 (t-90) REVERT: B 159 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8642 (mp) REVERT: B 246 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8936 (mp) REVERT: B 561 MET cc_start: 0.3386 (ptt) cc_final: 0.2478 (mmp) REVERT: C 92 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9128 (m) REVERT: D 143 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 406 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8265 (pp) REVERT: H 106 TRP cc_start: 0.8055 (t60) cc_final: 0.7656 (t-100) REVERT: L 51 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7178 (mm-30) outliers start: 136 outliers final: 96 residues processed: 382 average time/residue: 0.1394 time to fit residues: 91.1111 Evaluate side-chains 356 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 251 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 GLU Chi-restraints excluded: chain A residue 295 LEU 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 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 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 757 ILE Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN 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 125 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 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 228 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU 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 411 LEU 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 700 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 162 HIS 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 513 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 757 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 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 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 430 VAL 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 746 GLN Chi-restraints excluded: chain D residue 769 GLU 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 325 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 111 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 129 optimal weight: 9.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** 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 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** 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 = 0.4160 r_free = 0.4160 target = 0.162215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117796 restraints weight = 48546.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111178 restraints weight = 46261.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112049 restraints weight = 46000.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112662 restraints weight = 40178.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112794 restraints weight = 35565.637| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25562 Z= 0.190 Angle : 0.633 9.136 35040 Z= 0.325 Chirality : 0.044 0.266 4134 Planarity : 0.004 0.050 4523 Dihedral : 4.614 58.086 3774 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.77 % Favored : 86.81 % Rotamer: Outliers : 8.33 % Allowed : 31.81 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.15), residues: 3555 helix: 2.23 (0.15), residues: 1233 sheet: -1.97 (0.22), residues: 549 loop : -2.64 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 252 TYR 0.017 0.001 TYR L 50 PHE 0.038 0.002 PHE B 310 TRP 0.029 0.001 TRP H 106 HIS 0.008 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00462 (25542) covalent geometry : angle 0.63051 (35000) SS BOND : bond 0.00347 ( 20) SS BOND : angle 1.74280 ( 40) hydrogen bonds : bond 0.03681 ( 995) hydrogen bonds : angle 4.09627 ( 2886) *********************** 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 422 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 244 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7747 (t60) REVERT: A 526 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7718 (p90) REVERT: A 761 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8713 (t70) REVERT: B 44 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.5890 (t-90) REVERT: B 159 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9054 (mp) REVERT: B 246 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9010 (mp) REVERT: B 561 MET cc_start: 0.3475 (ptt) cc_final: 0.2430 (mmp) REVERT: C 92 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9141 (m) REVERT: C 158 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: D 143 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8429 (m) REVERT: D 153 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: D 387 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7383 (m90) REVERT: D 406 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8396 (pp) REVERT: H 106 TRP cc_start: 0.8194 (t60) cc_final: 0.7884 (t60) REVERT: L 51 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7347 (mm-30) outliers start: 178 outliers final: 136 residues processed: 400 average time/residue: 0.1382 time to fit residues: 95.1480 Evaluate side-chains 388 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 240 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 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 431 VAL Chi-restraints excluded: chain A residue 442 THR 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 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 712 TRP 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 98 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 125 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 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 259 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR 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 463 ILE 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 697 LEU Chi-restraints excluded: chain B residue 700 LEU 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 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU 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 246 VAL 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 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 528 GLU 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 757 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 153 GLN 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 278 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP 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 418 ILE 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 688 PHE 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 54 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 7 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** 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 = 0.4175 r_free = 0.4175 target = 0.163611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118425 restraints weight = 48606.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112475 restraints weight = 43901.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113170 restraints weight = 41466.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113607 restraints weight = 39774.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113786 restraints weight = 35154.575| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25562 Z= 0.149 Angle : 0.602 10.466 35040 Z= 0.308 Chirality : 0.043 0.238 4134 Planarity : 0.004 0.052 4523 Dihedral : 4.548 58.917 3774 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.62 % Favored : 87.99 % Rotamer: Outliers : 8.75 % Allowed : 31.52 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.15), residues: 3555 helix: 2.25 (0.15), residues: 1233 sheet: -1.90 (0.23), residues: 533 loop : -2.66 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 252 TYR 0.016 0.001 TYR L 50 PHE 0.036 0.001 PHE B 310 TRP 0.028 0.001 TRP H 106 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00359 (25542) covalent geometry : angle 0.60069 (35000) SS BOND : bond 0.00281 ( 20) SS BOND : angle 1.44967 ( 40) hydrogen bonds : bond 0.03275 ( 995) hydrogen bonds : angle 3.96818 ( 2886) *********************** 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 437 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 250 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.7649 (t60) REVERT: A 526 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7691 (p90) REVERT: A 761 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8692 (t70) REVERT: B 44 HIS cc_start: 0.6504 (OUTLIER) cc_final: 0.5935 (t-90) REVERT: B 159 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8998 (mp) REVERT: B 219 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8883 (tt) REVERT: B 246 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8994 (mp) REVERT: B 561 MET cc_start: 0.3426 (ptt) cc_final: 0.2464 (mmp) REVERT: C 92 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9127 (m) REVERT: C 158 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: C 648 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7698 (tp) REVERT: D 115 PHE cc_start: 0.9225 (t80) cc_final: 0.9002 (t80) REVERT: D 143 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8369 (m) REVERT: D 387 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7335 (m90) REVERT: D 406 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8331 (pp) REVERT: H 106 TRP cc_start: 0.8294 (t60) cc_final: 0.7979 (t60) REVERT: L 51 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7266 (mm-30) outliers start: 187 outliers final: 150 residues processed: 414 average time/residue: 0.1405 time to fit residues: 100.7524 Evaluate side-chains 406 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 243 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 140 THR 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 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 442 THR 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 527 ILE 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 712 TRP Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 125 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 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 219 LEU Chi-restraints excluded: chain B residue 228 LEU 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 319 SER Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 411 LEU 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 463 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 682 HIS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 728 VAL 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 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 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 183 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL 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 473 THR Chi-restraints excluded: chain C residue 486 THR 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 728 VAL Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 757 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 161 ILE 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 278 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 349 SER 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 411 LEU Chi-restraints excluded: chain D residue 418 ILE 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 513 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 727 LEU 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 54 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 184 optimal weight: 0.9990 chunk 173 optimal weight: 0.0370 chunk 244 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 242 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 343 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 686 HIS A 763 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** 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 = 0.4203 r_free = 0.4203 target = 0.166078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120690 restraints weight = 49603.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116267 restraints weight = 39129.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116445 restraints weight = 41113.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117209 restraints weight = 37472.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117411 restraints weight = 32686.697| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1469 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= 0.102 Angle : 0.573 9.754 35040 Z= 0.291 Chirality : 0.042 0.278 4134 Planarity : 0.003 0.052 4523 Dihedral : 4.330 58.343 3774 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.75 % Favored : 88.89 % Rotamer: Outliers : 6.88 % Allowed : 33.49 % Favored : 59.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 3555 helix: 2.39 (0.15), residues: 1224 sheet: -1.61 (0.24), residues: 515 loop : -2.63 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 252 TYR 0.016 0.001 TYR L 50 PHE 0.046 0.001 PHE B 310 TRP 0.025 0.001 TRP H 106 HIS 0.003 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00237 (25542) covalent geometry : angle 0.57130 (35000) SS BOND : bond 0.00208 ( 20) SS BOND : angle 1.32185 ( 40) hydrogen bonds : bond 0.02716 ( 995) hydrogen bonds : angle 3.77882 ( 2886) *********************** 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 406 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 259 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 315 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7588 (t60) REVERT: A 526 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7545 (p90) REVERT: A 654 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8491 (mmm160) REVERT: A 761 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8692 (t70) REVERT: B 44 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6163 (t-90) REVERT: B 159 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8744 (mp) REVERT: B 246 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 561 MET cc_start: 0.3408 (ptt) cc_final: 0.2470 (mmp) REVERT: C 158 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: C 648 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7664 (tp) REVERT: D 115 PHE cc_start: 0.9150 (t80) cc_final: 0.8899 (t80) REVERT: D 146 GLN cc_start: 0.8650 (mp10) cc_final: 0.8426 (mp10) REVERT: D 218 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: D 406 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8207 (pp) REVERT: H 106 TRP cc_start: 0.8202 (t60) cc_final: 0.7980 (t60) REVERT: L 51 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7117 (mm-30) outliers start: 147 outliers final: 114 residues processed: 386 average time/residue: 0.1453 time to fit residues: 95.6674 Evaluate side-chains 374 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 249 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 140 THR 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 315 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER 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 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 125 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 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 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 348 LEU Chi-restraints excluded: chain B residue 411 LEU 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 463 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 682 HIS 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 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 513 ILE 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 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 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 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 THR 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 513 THR Chi-restraints excluded: chain D residue 660 PHE 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 54 HIS 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 308 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 131 optimal weight: 40.0000 chunk 135 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 331 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 114 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.166460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122315 restraints weight = 49664.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116599 restraints weight = 42350.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117530 restraints weight = 39771.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117904 restraints weight = 36245.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118119 restraints weight = 33067.135| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25562 Z= 0.103 Angle : 0.574 10.257 35040 Z= 0.291 Chirality : 0.042 0.259 4134 Planarity : 0.003 0.050 4523 Dihedral : 4.233 58.516 3774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.80 % Favored : 88.83 % Rotamer: Outliers : 6.74 % Allowed : 33.77 % Favored : 59.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3555 helix: 2.45 (0.15), residues: 1222 sheet: -1.60 (0.24), residues: 508 loop : -2.60 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 36 TYR 0.016 0.001 TYR L 50 PHE 0.045 0.001 PHE B 310 TRP 0.022 0.001 TRP H 106 HIS 0.003 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00240 (25542) covalent geometry : angle 0.57268 (35000) SS BOND : bond 0.00205 ( 20) SS BOND : angle 1.29410 ( 40) hydrogen bonds : bond 0.02693 ( 995) hydrogen bonds : angle 3.72321 ( 2886) *********************** 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 405 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 261 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 315 TRP cc_start: 0.8208 (OUTLIER) cc_final: 0.7599 (t60) REVERT: A 526 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7522 (p90) REVERT: A 654 ARG cc_start: 0.8960 (mtp-110) cc_final: 0.8479 (mmm160) REVERT: B 44 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6131 (t-90) REVERT: B 159 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 219 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8877 (tt) REVERT: B 246 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8925 (mp) REVERT: B 561 MET cc_start: 0.3388 (ptt) cc_final: 0.2453 (mmp) REVERT: C 158 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: C 648 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7670 (tp) REVERT: C 743 MET cc_start: 0.8550 (mmm) cc_final: 0.8262 (mmm) REVERT: D 112 MET cc_start: 0.8778 (tpp) cc_final: 0.8529 (tpp) REVERT: D 115 PHE cc_start: 0.9138 (t80) cc_final: 0.8900 (t80) REVERT: D 143 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8386 (m) REVERT: D 146 GLN cc_start: 0.8605 (mp10) cc_final: 0.8394 (mp10) REVERT: D 218 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: D 379 GLU cc_start: 0.7343 (tp30) cc_final: 0.7014 (tp30) REVERT: D 406 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8187 (pp) REVERT: L 51 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 144 outliers final: 123 residues processed: 385 average time/residue: 0.1398 time to fit residues: 92.4479 Evaluate side-chains 392 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 257 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 379 ILE 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 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 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 69 VAL Chi-restraints excluded: chain B residue 125 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 215 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 228 LEU 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 348 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 411 LEU 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 463 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 682 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 728 VAL 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 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 473 THR Chi-restraints excluded: chain C residue 486 THR 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 728 VAL 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 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 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 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 278 SER Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 418 ILE 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 513 THR Chi-restraints excluded: chain D residue 660 PHE 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 38 VAL Chi-restraints excluded: chain H residue 54 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 72 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** H 33 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.166550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127524 restraints weight = 49957.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121399 restraints weight = 60257.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122934 restraints weight = 56602.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123175 restraints weight = 43451.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123227 restraints weight = 38957.767| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25562 Z= 0.131 Angle : 0.594 9.389 35040 Z= 0.301 Chirality : 0.043 0.274 4134 Planarity : 0.004 0.050 4523 Dihedral : 4.298 58.923 3774 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.36 % Favored : 88.27 % Rotamer: Outliers : 6.59 % Allowed : 33.54 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3555 helix: 2.47 (0.15), residues: 1225 sheet: -1.69 (0.23), residues: 523 loop : -2.59 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 36 TYR 0.012 0.001 TYR L 50 PHE 0.047 0.001 PHE B 310 TRP 0.047 0.001 TRP H 106 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00315 (25542) covalent geometry : angle 0.59267 (35000) SS BOND : bond 0.00238 ( 20) SS BOND : angle 1.31166 ( 40) hydrogen bonds : bond 0.02995 ( 995) hydrogen bonds : angle 3.77506 ( 2886) ********************** 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 395 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 254 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7533 (t60) REVERT: A 526 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7626 (p90) REVERT: A 654 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.7658 (ttm110) REVERT: B 159 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8662 (mp) REVERT: B 219 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8893 (tt) REVERT: B 246 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8979 (mp) REVERT: B 561 MET cc_start: 0.3505 (ptt) cc_final: 0.2252 (mmp) REVERT: C 158 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: C 648 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7626 (tp) REVERT: D 115 PHE cc_start: 0.9098 (t80) cc_final: 0.8860 (t80) REVERT: D 143 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8389 (m) REVERT: D 406 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8251 (pp) REVERT: L 51 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7252 (mm-30) outliers start: 141 outliers final: 125 residues processed: 376 average time/residue: 0.1421 time to fit residues: 91.9594 Evaluate side-chains 386 residues out of total 3119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 252 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 352 SER Chi-restraints excluded: chain A residue 379 ILE 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 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 743 MET 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 125 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 215 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 228 LEU 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 348 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 411 LEU 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 463 ILE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 682 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 728 VAL 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 255 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR 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 728 VAL 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 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 278 SER Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 418 ILE 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 660 PHE 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 H residue 22 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 54 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 339 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 316 optimal weight: 6.9990 chunk 204 optimal weight: 0.5980 chunk 209 optimal weight: 5.9990 chunk 353 optimal weight: 50.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** H 33 ASN ** 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 = 0.4196 r_free = 0.4196 target = 0.165139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121481 restraints weight = 49635.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115938 restraints weight = 42392.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116900 restraints weight = 40831.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117354 restraints weight = 38064.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117591 restraints weight = 33110.107| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1662 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= 0.114 Angle : 0.585 11.704 35040 Z= 0.295 Chirality : 0.043 0.268 4134 Planarity : 0.003 0.051 4523 Dihedral : 4.246 59.455 3774 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.77 % Favored : 88.86 % Rotamer: Outliers : 6.55 % Allowed : 33.58 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.15), residues: 3555 helix: 2.46 (0.15), residues: 1227 sheet: -1.58 (0.24), residues: 514 loop : -2.61 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 36 TYR 0.020 0.001 TYR L 50 PHE 0.046 0.001 PHE B 310 TRP 0.045 0.001 TRP H 106 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00272 (25542) covalent geometry : angle 0.58334 (35000) SS BOND : bond 0.00213 ( 20) SS BOND : angle 1.25679 ( 40) hydrogen bonds : bond 0.02744 ( 995) hydrogen bonds : angle 3.71032 ( 2886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4755.99 seconds wall clock time: 82 minutes 32.81 seconds (4952.81 seconds total)