Starting phenix.real_space_refine on Mon May 4 03:50:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usw_42520/05_2026/8usw_42520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usw_42520/05_2026/8usw_42520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8usw_42520/05_2026/8usw_42520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usw_42520/05_2026/8usw_42520.map" model { file = "/net/cci-nas-00/data/ceres_data/8usw_42520/05_2026/8usw_42520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usw_42520/05_2026/8usw_42520.cif" } resolution = 4.23 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= 0.001 sd= 0.013 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 63 5.16 5 C 11070 2.51 5 N 3337 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17975 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 4434 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 693} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1397 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1170 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'ASN:plan1': 23, 'ARG:plan': 24, 'HIS:plan': 14, 'GLU:plan': 28, 'GLN:plan1': 15, 'PHE:plan': 13, 'TRP:plan': 8, 'ASP:plan': 19, 'TYR:plan': 15} Unresolved non-hydrogen planarities: 743 Chain: "B" Number of atoms: 4528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 4528 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1405 Unresolved non-hydrogen angles: 1822 Unresolved non-hydrogen dihedrals: 1164 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 16, 'HIS:plan': 12, 'ASP:plan': 16, 'PHE:plan': 24, 'ASN:plan1': 23, 'GLU:plan': 25, 'TYR:plan': 7, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 715 Chain: "C" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 4447 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 693} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1384 Unresolved non-hydrogen angles: 1783 Unresolved non-hydrogen dihedrals: 1159 Unresolved non-hydrogen chiralities: 133 Planarities with less than four sites: {'ASN:plan1': 22, 'ARG:plan': 25, 'HIS:plan': 13, 'GLU:plan': 27, 'GLN:plan1': 16, 'PHE:plan': 13, 'TRP:plan': 8, 'ASP:plan': 18, 'TYR:plan': 15} Unresolved non-hydrogen planarities: 737 Chain: "D" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 4532 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 1814 Unresolved non-hydrogen dihedrals: 1159 Unresolved non-hydrogen chiralities: 157 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 17, 'HIS:plan': 12, 'ASP:plan': 16, 'PHE:plan': 24, 'ASN:plan1': 23, 'GLU:plan': 25, 'TYR:plan': 6, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 713 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.26 Number of scatterers: 17975 At special positions: 0 Unit cell: (118.128, 169.488, 194.312, 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 63 16.00 O 3505 8.00 N 3337 7.00 C 11070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.04 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.04 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 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.02 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.04 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 873.9 milliseconds 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 29 sheets defined 41.2% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 34 through 52 removed outlier: 4.002A pdb=" N HIS A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.920A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.257A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 removed outlier: 3.800A pdb=" N ARG A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.907A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.601A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.846A pdb=" N GLU A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 212 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.050A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.060A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.538A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.763A pdb=" N GLY A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.768A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 removed outlier: 4.108A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 658 Processing helix chain 'A' and resid 670 through 674 removed outlier: 3.547A pdb=" N ARG A 673 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 674 " --> pdb=" O ARG A 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 670 through 674' Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.600A pdb=" N TYR A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 700 removed outlier: 3.737A pdb=" N SER A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 700' Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.892A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 781 removed outlier: 3.880A pdb=" N VAL A 772 " --> pdb=" O TRP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 176 through 192 removed outlier: 3.977A pdb=" N PHE B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.627A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.968A pdb=" N ASN B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.822A pdb=" N PHE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 407 removed outlier: 3.506A pdb=" N TYR B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 614 through 621 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 741 through 769 Processing helix chain 'B' and resid 802 through 808 removed outlier: 4.194A pdb=" N VAL B 806 " --> pdb=" O ALA B 802 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 808 " --> pdb=" O ASP B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 817 Processing helix chain 'B' and resid 825 through 834 removed outlier: 3.609A pdb=" N LYS B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 853 Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 885 through 898 removed outlier: 3.530A pdb=" N GLY B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 908 removed outlier: 3.722A pdb=" N LEU B 903 " --> pdb=" O PHE B 899 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 908 " --> pdb=" O HIS B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 955 Processing helix chain 'C' and resid 34 through 53 removed outlier: 4.058A pdb=" N HIS C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.808A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 155 removed outlier: 3.840A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 4.187A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.971A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.595A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.630A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 458 through 469 removed outlier: 3.786A pdb=" N LEU C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 558 through 579 removed outlier: 4.047A pdb=" N LEU C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 657 Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.873A pdb=" N ASN C 674 " --> pdb=" O ARG C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 693 removed outlier: 3.764A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.507A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 removed outlier: 3.545A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.502A pdb=" N LEU C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 782 Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.773A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.661A pdb=" N ARG D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.936A pdb=" N PHE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 276 through 286 removed outlier: 3.588A pdb=" N ASN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 Processing helix chain 'D' and resid 331 through 346 removed outlier: 3.578A pdb=" N PHE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 384 through 405 Processing helix chain 'D' and resid 407 through 413 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.657A pdb=" N ARG D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 562 Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.536A pdb=" N PHE D 572 " --> pdb=" O PRO D 569 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 573 " --> pdb=" O ILE D 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 616 through 622 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.638A pdb=" N SER D 639 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 767 Processing helix chain 'D' and resid 782 through 787 Processing helix chain 'D' and resid 800 through 810 removed outlier: 3.737A pdb=" N ASP D 804 " --> pdb=" O SER D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 818 removed outlier: 3.569A pdb=" N ARG D 818 " --> pdb=" O HIS D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 834 Processing helix chain 'D' and resid 883 through 897 removed outlier: 3.649A pdb=" N ILE D 887 " --> pdb=" O LEU D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 908 removed outlier: 3.677A pdb=" N TYR D 908 " --> pdb=" O HIS D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 954 removed outlier: 3.794A pdb=" N ILE D 954 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 7.147A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 6.676A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.580A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.461A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 513 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 761 " --> pdb=" O ILE A 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 removed outlier: 4.172A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.190A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 541 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 539 " --> pdb=" O TRP A 731 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 152 removed outlier: 6.181A pdb=" N VAL B 48 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL B 151 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 50 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 12.348A pdb=" N ALA B 47 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ALA B 195 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG B 49 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU B 197 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY B 51 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE B 221 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 196 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 198 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ARG B 225 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL B 220 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 240 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER B 222 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 242 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL B 224 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL B 457 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN B 239 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER B 459 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N SER B 241 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 295 removed outlier: 7.171A pdb=" N PHE B 265 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE B 294 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 267 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.300A pdb=" N HIS B 377 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP B 358 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LYS B 379 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN B 467 " --> pdb=" O ARG B 480 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG B 480 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN B 469 " --> pdb=" O TRP B 478 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP B 478 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.060A pdb=" N LEU B 513 " --> pdb=" O ASP B 594 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 518 through 519 removed outlier: 3.760A pdb=" N THR B 519 " --> pdb=" O TYR B 598 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 541 through 544 Processing sheet with id=AB5, first strand: chain 'B' and resid 842 through 845 removed outlier: 3.704A pdb=" N MET B 844 " --> pdb=" O GLY B 654 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 654 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 655 " --> pdb=" O VAL B 864 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 864 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 26 through 32 removed outlier: 4.208A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 31 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AB8, first strand: chain 'C' and resid 194 through 196 removed outlier: 6.514A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 351 through 357 removed outlier: 6.420A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.798A pdb=" N GLU C 475 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 400 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 434 through 437 Processing sheet with id=AC3, first strand: chain 'C' and resid 513 through 517 removed outlier: 3.521A pdb=" N ILE C 513 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY C 761 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 730 through 731 removed outlier: 3.549A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 753 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 148 through 152 removed outlier: 6.311A pdb=" N VAL D 48 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 151 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 50 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ARG D 49 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU D 196 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY D 51 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA D 198 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE D 221 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU D 196 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA D 198 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 290 through 291 removed outlier: 8.156A pdb=" N ILE D 295 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU D 267 " --> pdb=" O ILE D 295 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 290 through 291 removed outlier: 4.768A pdb=" N THR D 324 " --> pdb=" O ASN D 264 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS D 377 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP D 358 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LYS D 379 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 374 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE D 463 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER D 483 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE D 465 " --> pdb=" O LEU D 481 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 441 through 443 Processing sheet with id=AC9, first strand: chain 'D' and resid 514 through 519 removed outlier: 6.357A pdb=" N LEU D 515 " --> pdb=" O ASP D 596 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR D 598 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 517 " --> pdb=" O TYR D 598 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 542 " --> pdb=" O PHE D 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 597 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 544 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 599 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 606 through 609 removed outlier: 3.789A pdb=" N ALA D 607 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR D 614 " --> pdb=" O ALA D 607 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 821 through 822 removed outlier: 8.765A pdb=" N VAL D 822 " --> pdb=" O PHE D 794 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR D 796 " --> pdb=" O VAL D 822 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 795 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 843 " --> pdb=" O GLY D 795 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL D 797 " --> pdb=" O ILE D 843 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N ASP D 845 " --> pdb=" O VAL D 797 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET D 844 " --> pdb=" O GLY D 654 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 654 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 657 " --> pdb=" O LEU D 862 " (cutoff:3.500A) 889 hydrogen bonds defined for protein. 2553 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: 3.02 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3319 1.29 - 1.43: 4266 1.43 - 1.56: 10505 1.56 - 1.69: 0 1.69 - 1.83: 98 Bond restraints: 18188 Sorted by residual: bond pdb=" C7 DQC C 901 " pdb=" C9 DQC C 901 " ideal model delta sigma weight residual 1.427 1.281 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C7 DQC A 901 " pdb=" C9 DQC A 901 " ideal model delta sigma weight residual 1.427 1.281 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" N ILE D 587 " pdb=" CA ILE D 587 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N ILE B 587 " pdb=" CA ILE B 587 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.59e+00 bond pdb=" N ARG D 622 " pdb=" CA ARG D 622 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.49e+00 ... (remaining 18183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 24565 2.66 - 5.31: 350 5.31 - 7.97: 39 7.97 - 10.63: 0 10.63 - 13.29: 3 Bond angle restraints: 24957 Sorted by residual: angle pdb=" C PHE C 484 " pdb=" CA PHE C 484 " pdb=" CB PHE C 484 " ideal model delta sigma weight residual 110.31 121.79 -11.48 2.09e+00 2.29e-01 3.02e+01 angle pdb=" N GLU B 830 " pdb=" CA GLU B 830 " pdb=" C GLU B 830 " ideal model delta sigma weight residual 112.90 106.88 6.02 1.31e+00 5.83e-01 2.11e+01 angle pdb=" N LYS D 846 " pdb=" CA LYS D 846 " pdb=" C LYS D 846 " ideal model delta sigma weight residual 112.97 108.45 4.52 1.06e+00 8.90e-01 1.82e+01 angle pdb=" N ARG B 622 " pdb=" CA ARG B 622 " pdb=" C ARG B 622 " ideal model delta sigma weight residual 113.15 108.36 4.79 1.19e+00 7.06e-01 1.62e+01 angle pdb=" CA LEU A 505 " pdb=" CB LEU A 505 " pdb=" CG LEU A 505 " ideal model delta sigma weight residual 116.30 103.01 13.29 3.50e+00 8.16e-02 1.44e+01 ... (remaining 24952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10130 17.92 - 35.85: 522 35.85 - 53.77: 81 53.77 - 71.69: 14 71.69 - 89.61: 8 Dihedral angle restraints: 10755 sinusoidal: 2274 harmonic: 8481 Sorted by residual: dihedral pdb=" CA SER D 778 " pdb=" C SER D 778 " pdb=" N GLY D 779 " pdb=" CA GLY D 779 " ideal model delta harmonic sigma weight residual 180.00 -144.41 -35.59 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 575 " pdb=" CB CYS B 575 " ideal model delta sinusoidal sigma weight residual 93.00 154.34 -61.34 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CA MET B 817 " pdb=" C MET B 817 " pdb=" N ARG B 818 " pdb=" CA ARG B 818 " ideal model delta harmonic sigma weight residual 180.00 -149.14 -30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 10752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2666 0.074 - 0.149: 373 0.149 - 0.223: 14 0.223 - 0.297: 1 0.297 - 0.372: 2 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA PHE C 484 " pdb=" N PHE C 484 " pdb=" C PHE C 484 " pdb=" CB PHE C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB ILE A 760 " pdb=" CA ILE A 760 " pdb=" CG1 ILE A 760 " pdb=" CG2 ILE A 760 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA MET B 902 " pdb=" N MET B 902 " pdb=" C MET B 902 " pdb=" CB MET B 902 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3053 not shown) Planarity restraints: 3421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 527 " 0.025 2.00e-02 2.50e+03 2.43e-02 1.03e+01 pdb=" CG PHE D 527 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE D 527 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 527 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 527 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 527 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 527 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 DQC A 901 " -0.002 2.00e-02 2.50e+03 1.81e-02 9.00e+00 pdb=" C4 DQC A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DQC A 901 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DQC A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DQC A 901 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DQC A 901 " -0.002 2.00e-02 2.50e+03 pdb=" C9 DQC A 901 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DQC A 901 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DQC A 901 " 0.014 2.00e-02 2.50e+03 pdb=" N4 DQC A 901 " -0.012 2.00e-02 2.50e+03 pdb=" N8 DQC A 901 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 483 " 0.014 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C LYS A 483 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS A 483 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 484 " 0.017 2.00e-02 2.50e+03 ... (remaining 3418 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 91 2.44 - 3.06: 12907 3.06 - 3.67: 26127 3.67 - 4.29: 32267 4.29 - 4.90: 52542 Nonbonded interactions: 123934 Sorted by model distance: nonbonded pdb=" OD2 ASP C 732 " pdb=" O6 DQC C 901 " model vdw 1.827 3.040 nonbonded pdb=" OE1 GLN C 405 " pdb=" CZ PHE C 484 " model vdw 1.861 3.340 nonbonded pdb=" NZ LYS B 586 " pdb=" CE2 TYR B 894 " model vdw 1.913 3.420 nonbonded pdb=" O THR B 553 " pdb=" OG SER B 556 " model vdw 1.936 3.040 nonbonded pdb=" OD1 ASP A 732 " pdb=" O6 DQC A 901 " model vdw 2.039 3.040 ... (remaining 123929 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 25 through 486 or (resid 487 and (name N or name CA or nam \ e C or name O or name CB )) or resid 488 through 561 or (resid 562 through 566 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 567 through 66 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 663 through \ 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) or re \ sid 707 through 765 or (resid 766 and (name N or name CA or name C or name O or \ name CB )) or resid 767 through 901)) selection = (chain 'C' and (resid 25 through 395 or (resid 396 and (name N or name CA or nam \ e C or name O or name CB )) or resid 397 through 405 or (resid 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 through 439 or (resid 4 \ 40 through 444 and (name N or name CA or name C or name O or name CB )) or (resi \ d 445 through 449 and (name N or name CA or name C or name O or name CB )) or re \ sid 450 through 495 or (resid 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 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 (resid 543 through 546 an \ d (name N or name CA or name C or name O or name CB )) or resid 547 through 677 \ or (resid 678 and (name N or name CA or name C or name O or name CB )) or resid \ 679 through 697 or (resid 698 and (name N or name CA or name C or name O or name \ CB )) or resid 699 through 901)) } ncs_group { reference = (chain 'B' and (resid 38 through 659 or (resid 660 through 741 and (name N or na \ me CA or name C or name O or name CB )) or resid 742 through 955)) selection = (chain 'D' and (resid 38 through 773 or (resid 774 through 775 and (name N or na \ me CA or name C or name O or name CB )) or resid 776 through 869 or (resid 870 a \ nd (name N or name CA or name C or name O or name CB )) or resid 871 through 955 \ )) } 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: 4.420 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.770 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 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 : 0.009 0.557 18202 Z= 0.661 Angle : 0.774 13.285 24981 Z= 0.429 Chirality : 0.049 0.372 3056 Planarity : 0.005 0.064 3421 Dihedral : 12.046 89.613 5211 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.33 % Favored : 90.29 % Rotamer: Outliers : 1.10 % Allowed : 0.70 % Favored : 98.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2914 helix: 1.89 (0.17), residues: 1082 sheet: -1.00 (0.26), residues: 400 loop : -1.85 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 673 TYR 0.020 0.002 TYR B 579 PHE 0.056 0.003 PHE D 527 TRP 0.021 0.002 TRP C 731 HIS 0.007 0.002 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00718 (18188) covalent geometry : angle 0.77212 (24957) SS BOND : bond 0.00684 ( 12) SS BOND : angle 1.71903 ( 24) hydrogen bonds : bond 0.17313 ( 888) hydrogen bonds : angle 6.49548 ( 2553) Misc. bond : bond 0.54619 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 484 PHE cc_start: 0.8525 (m-80) cc_final: 0.7983 (m-10) REVERT: B 544 LEU cc_start: 0.9105 (tp) cc_final: 0.8844 (tt) REVERT: B 813 MET cc_start: 0.8488 (ppp) cc_final: 0.8156 (ppp) REVERT: B 909 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7209 (ttm110) REVERT: D 514 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7522 (m-70) REVERT: D 845 ASP cc_start: 0.8201 (m-30) cc_final: 0.7997 (m-30) outliers start: 11 outliers final: 2 residues processed: 175 average time/residue: 0.1094 time to fit residues: 31.7706 Evaluate side-chains 149 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 HIS D 626 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.132718 restraints weight = 59166.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.126366 restraints weight = 79684.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.123944 restraints weight = 107617.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.124817 restraints weight = 90370.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.124165 restraints weight = 67913.170| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18202 Z= 0.129 Angle : 0.550 6.190 24981 Z= 0.301 Chirality : 0.044 0.212 3056 Planarity : 0.004 0.057 3421 Dihedral : 4.549 31.237 3041 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.00 % Favored : 92.66 % Rotamer: Outliers : 0.10 % Allowed : 6.33 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2914 helix: 2.21 (0.16), residues: 1123 sheet: -0.81 (0.27), residues: 381 loop : -1.86 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 909 TYR 0.034 0.002 TYR B 894 PHE 0.020 0.002 PHE D 527 TRP 0.012 0.001 TRP B 907 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00272 (18188) covalent geometry : angle 0.54930 (24957) SS BOND : bond 0.00307 ( 12) SS BOND : angle 0.93711 ( 24) hydrogen bonds : bond 0.03573 ( 888) hydrogen bonds : angle 4.66730 ( 2553) Misc. bond : bond 0.00503 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: B 651 THR cc_start: 0.8597 (t) cc_final: 0.8368 (t) REVERT: B 813 MET cc_start: 0.8504 (ppp) cc_final: 0.7647 (ppp) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.0979 time to fit residues: 31.4243 Evaluate side-chains 146 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 104 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 168 optimal weight: 50.0000 chunk 77 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 14 optimal weight: 40.0000 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 0.1980 chunk 278 optimal weight: 0.7980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS A 719 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS D 821 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.147828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.127767 restraints weight = 59640.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.122617 restraints weight = 87135.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120115 restraints weight = 93690.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120278 restraints weight = 83047.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.119064 restraints weight = 66946.473| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 18202 Z= 0.281 Angle : 0.673 9.908 24981 Z= 0.360 Chirality : 0.047 0.185 3056 Planarity : 0.004 0.057 3421 Dihedral : 4.772 32.300 3041 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.99 % Favored : 90.63 % Rotamer: Outliers : 0.10 % Allowed : 9.04 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2914 helix: 2.20 (0.16), residues: 1122 sheet: -1.02 (0.27), residues: 381 loop : -1.90 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 673 TYR 0.028 0.002 TYR B 894 PHE 0.044 0.003 PHE D 527 TRP 0.014 0.002 TRP A 792 HIS 0.008 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00635 (18188) covalent geometry : angle 0.67287 (24957) SS BOND : bond 0.00930 ( 12) SS BOND : angle 1.12755 ( 24) hydrogen bonds : bond 0.03725 ( 888) hydrogen bonds : angle 4.58893 ( 2553) Misc. bond : bond 0.00185 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9086 (tp) cc_final: 0.8721 (tt) REVERT: B 651 THR cc_start: 0.8525 (t) cc_final: 0.8282 (t) REVERT: B 813 MET cc_start: 0.8809 (ppp) cc_final: 0.7847 (ppp) REVERT: B 845 ASP cc_start: 0.8403 (t0) cc_final: 0.8183 (t0) REVERT: C 512 MET cc_start: 0.8630 (mmp) cc_final: 0.8416 (mmp) REVERT: D 585 GLU cc_start: 0.8020 (tp30) cc_final: 0.7660 (tt0) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.0912 time to fit residues: 27.1350 Evaluate side-chains 140 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 119 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 117 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 259 optimal weight: 0.0870 chunk 174 optimal weight: 10.0000 overall best weight: 1.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 705 HIS ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.149336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.128248 restraints weight = 58537.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.121954 restraints weight = 88551.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.118738 restraints weight = 86320.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.119007 restraints weight = 73737.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.118550 restraints weight = 57773.930| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18202 Z= 0.162 Angle : 0.556 6.680 24981 Z= 0.301 Chirality : 0.045 0.265 3056 Planarity : 0.004 0.058 3421 Dihedral : 4.459 30.291 3041 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.21 % Favored : 92.42 % Rotamer: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2914 helix: 2.35 (0.16), residues: 1128 sheet: -1.00 (0.26), residues: 397 loop : -1.81 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 793 TYR 0.041 0.002 TYR B 816 PHE 0.021 0.002 PHE D 527 TRP 0.010 0.001 TRP B 907 HIS 0.008 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00366 (18188) covalent geometry : angle 0.55552 (24957) SS BOND : bond 0.00446 ( 12) SS BOND : angle 0.96690 ( 24) hydrogen bonds : bond 0.02997 ( 888) hydrogen bonds : angle 4.21873 ( 2553) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.8650 (m-80) cc_final: 0.8317 (m-80) REVERT: B 544 LEU cc_start: 0.9006 (tp) cc_final: 0.8631 (tt) REVERT: B 813 MET cc_start: 0.8717 (ppp) cc_final: 0.7555 (ppp) REVERT: C 736 LEU cc_start: 0.9368 (mt) cc_final: 0.9111 (tp) REVERT: D 514 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: D 585 GLU cc_start: 0.7968 (tp30) cc_final: 0.7646 (tt0) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.0912 time to fit residues: 28.3186 Evaluate side-chains 151 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 149 optimal weight: 50.0000 chunk 157 optimal weight: 0.0060 chunk 160 optimal weight: 20.0000 chunk 257 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 143 optimal weight: 0.1980 chunk 237 optimal weight: 50.0000 chunk 142 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN C 705 HIS D 781 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.151933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.132505 restraints weight = 59721.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.127009 restraints weight = 90585.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.123618 restraints weight = 93743.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.123938 restraints weight = 82772.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123641 restraints weight = 60381.923| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18202 Z= 0.103 Angle : 0.509 8.302 24981 Z= 0.276 Chirality : 0.043 0.179 3056 Planarity : 0.003 0.057 3421 Dihedral : 4.153 27.710 3041 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.76 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2914 helix: 2.47 (0.16), residues: 1130 sheet: -0.86 (0.27), residues: 394 loop : -1.73 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 794 TYR 0.015 0.001 TYR B 894 PHE 0.020 0.001 PHE C 738 TRP 0.013 0.001 TRP B 907 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00220 (18188) covalent geometry : angle 0.50858 (24957) SS BOND : bond 0.00761 ( 12) SS BOND : angle 1.05142 ( 24) hydrogen bonds : bond 0.02629 ( 888) hydrogen bonds : angle 3.94588 ( 2553) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.8300 (m-80) cc_final: 0.8032 (m-80) REVERT: B 544 LEU cc_start: 0.8927 (tp) cc_final: 0.8589 (tt) REVERT: B 813 MET cc_start: 0.8596 (ppp) cc_final: 0.7312 (ppp) REVERT: C 512 MET cc_start: 0.8468 (mmp) cc_final: 0.8173 (mmp) REVERT: D 585 GLU cc_start: 0.7968 (tp30) cc_final: 0.7660 (tt0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0945 time to fit residues: 32.1814 Evaluate side-chains 154 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 28 optimal weight: 4.9990 chunk 162 optimal weight: 0.0060 chunk 93 optimal weight: 40.0000 chunk 4 optimal weight: 50.0000 chunk 271 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 50.0000 chunk 205 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 453 GLN C 509 GLN D 514 HIS ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.150974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.130999 restraints weight = 59246.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.124453 restraints weight = 92863.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.121776 restraints weight = 89852.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.121288 restraints weight = 86406.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.121068 restraints weight = 69191.739| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18202 Z= 0.138 Angle : 0.530 6.608 24981 Z= 0.285 Chirality : 0.044 0.171 3056 Planarity : 0.004 0.056 3421 Dihedral : 4.139 26.865 3041 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.10 % Favored : 92.62 % Rotamer: Outliers : 0.20 % Allowed : 2.11 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2914 helix: 2.52 (0.16), residues: 1127 sheet: -0.84 (0.27), residues: 399 loop : -1.70 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 798 TYR 0.019 0.002 TYR B 816 PHE 0.021 0.002 PHE C 738 TRP 0.015 0.001 TRP C 731 HIS 0.010 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00309 (18188) covalent geometry : angle 0.52961 (24957) SS BOND : bond 0.00405 ( 12) SS BOND : angle 0.87598 ( 24) hydrogen bonds : bond 0.02681 ( 888) hydrogen bonds : angle 3.89071 ( 2553) Misc. bond : bond 0.00700 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 470 MET cc_start: 0.8515 (mmm) cc_final: 0.7011 (mtt) REVERT: A 484 PHE cc_start: 0.8411 (m-80) cc_final: 0.8167 (m-80) REVERT: B 544 LEU cc_start: 0.8881 (tp) cc_final: 0.8538 (tt) REVERT: C 484 PHE cc_start: 0.7508 (m-80) cc_final: 0.7190 (m-80) REVERT: D 514 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7088 (m-70) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.0943 time to fit residues: 30.1070 Evaluate side-chains 145 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 171 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 0.0000 chunk 159 optimal weight: 40.0000 chunk 0 optimal weight: 60.0000 chunk 291 optimal weight: 50.0000 chunk 145 optimal weight: 50.0000 chunk 224 optimal weight: 50.0000 chunk 123 optimal weight: 0.7980 chunk 181 optimal weight: 50.0000 chunk 218 optimal weight: 50.0000 overall best weight: 14.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 HIS B 640 GLN ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 HIS D 790 GLN ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.138565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.113335 restraints weight = 58138.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100909 restraints weight = 84720.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097911 restraints weight = 78361.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097510 restraints weight = 72853.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097455 restraints weight = 62608.431| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.248 18202 Z= 0.955 Angle : 1.458 24.941 24981 Z= 0.758 Chirality : 0.069 0.477 3056 Planarity : 0.010 0.245 3421 Dihedral : 7.003 43.334 3041 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.51 % Allowed : 13.62 % Favored : 85.86 % Rotamer: Outliers : 0.20 % Allowed : 7.23 % Favored : 92.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2914 helix: 0.99 (0.16), residues: 1134 sheet: -1.78 (0.28), residues: 369 loop : -2.45 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG D 807 TYR 0.054 0.006 TYR B 577 PHE 0.085 0.008 PHE A 693 TRP 0.074 0.007 TRP A 792 HIS 0.033 0.005 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.02160 (18188) covalent geometry : angle 1.45653 (24957) SS BOND : bond 0.01659 ( 12) SS BOND : angle 2.36260 ( 24) hydrogen bonds : bond 0.06287 ( 888) hydrogen bonds : angle 6.12037 ( 2553) Misc. bond : bond 0.00372 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8209 (mmm) cc_final: 0.7626 (mmm) REVERT: B 544 LEU cc_start: 0.9196 (tp) cc_final: 0.8767 (tt) REVERT: C 709 HIS cc_start: 0.6335 (t70) cc_final: 0.5964 (t70) REVERT: C 731 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7982 (t-100) REVERT: D 900 MET cc_start: 0.8975 (mmm) cc_final: 0.8759 (tpp) outliers start: 2 outliers final: 1 residues processed: 142 average time/residue: 0.0918 time to fit residues: 23.6590 Evaluate side-chains 132 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 289 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 56 optimal weight: 40.0000 chunk 229 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN C 536 GLN ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.148892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.128509 restraints weight = 59396.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.123378 restraints weight = 86748.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.120173 restraints weight = 87649.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.120346 restraints weight = 78824.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.119565 restraints weight = 61101.302| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18202 Z= 0.190 Angle : 0.677 9.888 24981 Z= 0.363 Chirality : 0.047 0.269 3056 Planarity : 0.004 0.070 3421 Dihedral : 5.319 37.919 3041 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.79 % Favored : 91.87 % Rotamer: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2914 helix: 1.85 (0.16), residues: 1138 sheet: -1.43 (0.28), residues: 366 loop : -2.12 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 909 TYR 0.045 0.002 TYR B 816 PHE 0.026 0.002 PHE D 632 TRP 0.023 0.002 TRP A 731 HIS 0.008 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00424 (18188) covalent geometry : angle 0.67295 (24957) SS BOND : bond 0.00620 ( 12) SS BOND : angle 2.46832 ( 24) hydrogen bonds : bond 0.03417 ( 888) hydrogen bonds : angle 4.52853 ( 2553) Misc. bond : bond 0.00184 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8591 (mmm) cc_final: 0.7487 (mtm) REVERT: B 813 MET cc_start: 0.8936 (ppp) cc_final: 0.8211 (ppp) REVERT: B 905 ASP cc_start: 0.7342 (t0) cc_final: 0.7094 (t0) REVERT: C 709 HIS cc_start: 0.6063 (t70) cc_final: 0.5699 (t70) REVERT: D 900 MET cc_start: 0.8359 (mmm) cc_final: 0.8128 (tpp) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.0903 time to fit residues: 28.7949 Evaluate side-chains 140 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 69 optimal weight: 0.0980 chunk 165 optimal weight: 50.0000 chunk 125 optimal weight: 1.9990 chunk 242 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 223 optimal weight: 50.0000 chunk 30 optimal weight: 50.0000 chunk 260 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 chunk 285 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS D 514 HIS ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.149588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.112653 restraints weight = 57975.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108332 restraints weight = 45511.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108688 restraints weight = 49151.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108963 restraints weight = 42914.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109401 restraints weight = 37263.349| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18202 Z= 0.117 Angle : 0.564 8.616 24981 Z= 0.303 Chirality : 0.045 0.254 3056 Planarity : 0.004 0.059 3421 Dihedral : 4.471 31.104 3041 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.72 % Favored : 91.94 % Rotamer: Outliers : 0.10 % Allowed : 0.80 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2914 helix: 2.27 (0.16), residues: 1134 sheet: -1.24 (0.27), residues: 387 loop : -1.93 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 622 TYR 0.014 0.002 TYR B 831 PHE 0.016 0.001 PHE A 693 TRP 0.013 0.002 TRP A 731 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00259 (18188) covalent geometry : angle 0.56175 (24957) SS BOND : bond 0.00436 ( 12) SS BOND : angle 1.79859 ( 24) hydrogen bonds : bond 0.02705 ( 888) hydrogen bonds : angle 3.99102 ( 2553) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8545 (mmm) cc_final: 0.7369 (mtm) REVERT: B 813 MET cc_start: 0.8665 (ppp) cc_final: 0.8385 (ppp) REVERT: D 514 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.7029 (m-70) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0934 time to fit residues: 29.0417 Evaluate side-chains 150 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 82 optimal weight: 9.9990 chunk 170 optimal weight: 50.0000 chunk 182 optimal weight: 40.0000 chunk 279 optimal weight: 4.9990 chunk 78 optimal weight: 50.0000 chunk 210 optimal weight: 0.8980 chunk 224 optimal weight: 50.0000 chunk 126 optimal weight: 50.0000 chunk 237 optimal weight: 50.0000 chunk 118 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN C 536 GLN ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.146245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.119027 restraints weight = 57422.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.106608 restraints weight = 68098.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103505 restraints weight = 62005.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103158 restraints weight = 60893.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103811 restraints weight = 47636.962| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 18202 Z= 0.288 Angle : 0.715 12.369 24981 Z= 0.377 Chirality : 0.048 0.250 3056 Planarity : 0.005 0.064 3421 Dihedral : 4.885 32.613 3041 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.27 % Favored : 90.39 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2914 helix: 2.12 (0.16), residues: 1139 sheet: -1.38 (0.28), residues: 383 loop : -1.93 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 468 TYR 0.023 0.002 TYR D 831 PHE 0.068 0.003 PHE D 527 TRP 0.033 0.003 TRP A 792 HIS 0.010 0.002 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00660 (18188) covalent geometry : angle 0.71364 (24957) SS BOND : bond 0.00724 ( 12) SS BOND : angle 1.71955 ( 24) hydrogen bonds : bond 0.03486 ( 888) hydrogen bonds : angle 4.31162 ( 2553) Misc. bond : bond 0.00176 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 THR cc_start: 0.6984 (m) cc_final: 0.6386 (m) REVERT: A 470 MET cc_start: 0.8629 (mmm) cc_final: 0.7550 (mtm) REVERT: B 813 MET cc_start: 0.8963 (ppp) cc_final: 0.7919 (ppp) REVERT: C 512 MET cc_start: 0.8630 (mmp) cc_final: 0.8237 (mmp) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.0918 time to fit residues: 27.5143 Evaluate side-chains 139 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 131 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 229 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 205 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 290 optimal weight: 50.0000 chunk 272 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 267 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.147659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.110386 restraints weight = 57780.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105420 restraints weight = 51420.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.105725 restraints weight = 45842.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.105984 restraints weight = 40206.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106199 restraints weight = 38053.816| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18202 Z= 0.185 Angle : 0.616 9.022 24981 Z= 0.327 Chirality : 0.046 0.239 3056 Planarity : 0.004 0.060 3421 Dihedral : 4.649 31.489 3041 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.37 % Favored : 91.28 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2914 helix: 2.18 (0.16), residues: 1146 sheet: -1.34 (0.28), residues: 385 loop : -1.90 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 468 TYR 0.030 0.002 TYR B 894 PHE 0.040 0.002 PHE D 527 TRP 0.012 0.001 TRP A 731 HIS 0.007 0.001 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00422 (18188) covalent geometry : angle 0.61366 (24957) SS BOND : bond 0.00576 ( 12) SS BOND : angle 1.70895 ( 24) hydrogen bonds : bond 0.03038 ( 888) hydrogen bonds : angle 4.13365 ( 2553) Misc. bond : bond 0.00148 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2748.96 seconds wall clock time: 48 minutes 1.22 seconds (2881.22 seconds total)