Starting phenix.real_space_refine on Fri Aug 7 02:38:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2026/8h1c_34427.cif" } resolution = 4.5 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= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 148 5.49 5 S 62 5.16 5 C 11199 2.51 5 N 3182 2.21 5 O 3892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18483 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7715 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7710 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 983, 7710 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 7861 Chain: "C" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 72, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 8, 'rna3p': 63, None: 1} Not linked: pdbres="GTP C 1 " pdbres=" C C 2 " Chain: "A" Number of atoms: 7688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Conformer: "B" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 bond proxies already assigned to first conformer: 7834 Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1520 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 70, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1} Not linked: pdbres="GTP D 1 " pdbres=" C D 2 " Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AALA B 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 940 " occ=0.50 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 5.65, per 1000 atoms: 0.31 Number of scatterers: 18483 At special positions: 0 Unit cell: (202.4, 160.6, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 148 15.00 O 3892 8.00 N 3182 7.00 C 11199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3694 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 15 sheets defined 48.0% alpha, 9.8% beta 33 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'B' and resid 73 through 89 removed outlier: 3.814A pdb=" N ILE B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.996A pdb=" N PHE B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 removed outlier: 4.121A pdb=" N LEU B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.985A pdb=" N GLU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 296 removed outlier: 4.112A pdb=" N ILE B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP B 285 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 321 removed outlier: 3.501A pdb=" N ALA B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 352 removed outlier: 4.153A pdb=" N ARG B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 418 removed outlier: 3.537A pdb=" N LYS B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.636A pdb=" N GLU B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 508 through 521 Proline residue: B 516 - end of helix removed outlier: 3.642A pdb=" N SER B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 591 removed outlier: 3.572A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 613 removed outlier: 3.875A pdb=" N HIS B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 607 " --> pdb=" O ARG B 603 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 610 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 613 " --> pdb=" O SER B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 631 removed outlier: 4.118A pdb=" N GLU B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 631 " --> pdb=" O GLN B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 650 removed outlier: 3.835A pdb=" N PHE B 647 " --> pdb=" O ASP B 644 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 649 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 650 " --> pdb=" O PHE B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 662 removed outlier: 3.684A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B 662 " --> pdb=" O VAL B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 716 removed outlier: 3.764A pdb=" N VAL B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 694 " --> pdb=" O GLU B 690 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 699 " --> pdb=" O LYS B 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 700 " --> pdb=" O GLY B 696 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 removed outlier: 4.402A pdb=" N LEU B 727 " --> pdb=" O ARG B 724 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 728 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER B 729 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 757 removed outlier: 5.064A pdb=" N ALA B 751 " --> pdb=" O GLU B 747 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 753 " --> pdb=" O THR B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 762 No H-bonds generated for 'chain 'B' and resid 760 through 762' Processing helix chain 'B' and resid 763 through 771 removed outlier: 3.664A pdb=" N ILE B 767 " --> pdb=" O MET B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.710A pdb=" N ALA B 779 " --> pdb=" O SER B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 786 removed outlier: 4.254A pdb=" N GLU B 785 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 786 " --> pdb=" O ILE B 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 781 through 786' Processing helix chain 'B' and resid 787 through 790 Processing helix chain 'B' and resid 792 through 802 removed outlier: 3.517A pdb=" N GLY B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 813 removed outlier: 3.734A pdb=" N ALA B 808 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 809 " --> pdb=" O GLU B 805 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 810 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 848 removed outlier: 3.621A pdb=" N VAL B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 833 " --> pdb=" O PRO B 829 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 848 " --> pdb=" O GLY B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 874 Processing helix chain 'B' and resid 880 through 891 removed outlier: 4.096A pdb=" N THR B 886 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 887 " --> pdb=" O LYS B 883 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 891 " --> pdb=" O LEU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 917 removed outlier: 4.424A pdb=" N ILE B 901 " --> pdb=" O ASP B 897 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 930 removed outlier: 3.581A pdb=" N SER B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 951 removed outlier: 4.005A pdb=" N GLU B 946 " --> pdb=" O GLN B 942 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 948 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 949 " --> pdb=" O ILE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 964 removed outlier: 3.755A pdb=" N SER B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 971 removed outlier: 3.544A pdb=" N ILE B 970 " --> pdb=" O PRO B 966 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 971 " --> pdb=" O THR B 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 966 through 971' Processing helix chain 'B' and resid 974 through 978 Processing helix chain 'B' and resid 988 through 1003 removed outlier: 3.907A pdb=" N ARG B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1019 Processing helix chain 'B' and resid 1021 through 1032 removed outlier: 3.804A pdb=" N LEU B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B1027 " --> pdb=" O GLN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1054 Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.900A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.608A pdb=" N LEU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.629A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 256 through 273 removed outlier: 7.199A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.869A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 4.217A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 316 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.656A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.949A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.719A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.538A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.650A pdb=" N LYS A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.955A pdb=" N LEU A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.795A pdb=" N PHE A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 removed outlier: 4.193A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 716 removed outlier: 3.726A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 4.064A pdb=" N ARG A 724 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 725 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 726 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 728 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.790A pdb=" N GLU A 747 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 748 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.567A pdb=" N MET A 763 " --> pdb=" O ASN A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.793A pdb=" N LYS A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 773 " --> pdb=" O ASP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.589A pdb=" N THR A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.592A pdb=" N ARG A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 removed outlier: 3.594A pdb=" N ALA A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.760A pdb=" N ILE A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.808A pdb=" N LEU A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.695A pdb=" N LEU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.810A pdb=" N VAL A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.665A pdb=" N SER A 941 " --> pdb=" O PRO A 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 3.681A pdb=" N GLU A 961 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 removed outlier: 3.568A pdb=" N ARG A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 964 through 969' Processing helix chain 'A' and resid 990 through 1003 removed outlier: 4.417A pdb=" N SER A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.622A pdb=" N PHE A1014 " --> pdb=" O ASP A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1029 removed outlier: 3.595A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1055 removed outlier: 4.189A pdb=" N LEU A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.803A pdb=" N ALA B 122 " --> pdb=" O ALA B 91 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 153 current: chain 'B' and resid 193 through 202 removed outlier: 6.582A pdb=" N TRP B 194 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 208 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET B 202 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 425 through 430 removed outlier: 3.774A pdb=" N LEU B 434 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 390 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 440 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG B 384 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AA4, first strand: chain 'B' and resid 555 through 556 Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 565 Processing sheet with id=AA6, first strand: chain 'B' and resid 617 through 619 removed outlier: 7.056A pdb=" N PHE B 666 " --> pdb=" O CYS B 679 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS B 679 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL B 668 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET B 637 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 731 through 733 removed outlier: 6.322A pdb=" N GLY B 737 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92 removed outlier: 5.899A pdb=" N ALA A 91 " --> pdb=" O ALA A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 121 through 123 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'A' and resid 193 through 202 removed outlier: 6.427A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 216 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.906A pdb=" N ILE A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 425 through 427 removed outlier: 4.045A pdb=" N ASN A 440 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG A 384 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP A 542 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.574A pdb=" N LEU A 452 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 498 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR A 495 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG A 488 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 497 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AB4, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AB5, first strand: chain 'A' and resid 617 through 619 removed outlier: 7.198A pdb=" N PHE A 666 " --> pdb=" O CYS A 679 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 679 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL A 668 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 529 hydrogen bonds defined for protein. 1480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2788 1.30 - 1.43: 5741 1.43 - 1.56: 10228 1.56 - 1.68: 294 1.68 - 1.81: 104 Bond restraints: 19155 Sorted by residual: bond pdb=" C8 GTP D 1 " pdb=" N9 GTP D 1 " ideal model delta sigma weight residual 1.370 1.197 0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C8 GTP C 1 " pdb=" N9 GTP C 1 " ideal model delta sigma weight residual 1.370 1.198 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C4 GTP D 1 " pdb=" N9 GTP D 1 " ideal model delta sigma weight residual 1.375 1.214 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O2G GTP C 1 " pdb=" PG GTP C 1 " ideal model delta sigma weight residual 1.510 1.650 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" O2G GTP D 1 " pdb=" PG GTP D 1 " ideal model delta sigma weight residual 1.510 1.648 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 19150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 26193 2.87 - 5.74: 435 5.74 - 8.61: 42 8.61 - 11.48: 4 11.48 - 14.36: 3 Bond angle restraints: 26677 Sorted by residual: angle pdb=" N GLY A 737 " pdb=" CA GLY A 737 " pdb=" C GLY A 737 " ideal model delta sigma weight residual 111.56 119.88 -8.32 1.01e+00 9.80e-01 6.79e+01 angle pdb=" N ARG B 965 " pdb=" CA ARG B 965 " pdb=" C ARG B 965 " ideal model delta sigma weight residual 112.75 104.00 8.75 1.36e+00 5.41e-01 4.14e+01 angle pdb=" C VAL B1034 " pdb=" N MET B1035 " pdb=" CA MET B1035 " ideal model delta sigma weight residual 120.95 113.33 7.62 1.40e+00 5.10e-01 2.96e+01 angle pdb=" C4 GTP D 1 " pdb=" N9 GTP D 1 " pdb=" C8 GTP D 1 " ideal model delta sigma weight residual 108.00 122.36 -14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" CA ARG A 965 " pdb=" C ARG A 965 " pdb=" N PRO A 966 " ideal model delta sigma weight residual 118.44 125.95 -7.51 1.59e+00 3.96e-01 2.23e+01 ... (remaining 26672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 10792 35.69 - 71.38: 410 71.38 - 107.06: 22 107.06 - 142.75: 4 142.75 - 178.44: 2 Dihedral angle restraints: 11230 sinusoidal: 5516 harmonic: 5714 Sorted by residual: dihedral pdb=" C4' U D 31 " pdb=" C3' U D 31 " pdb=" C2' U D 31 " pdb=" C1' U D 31 " ideal model delta sinusoidal sigma weight residual 36.35 -38.05 74.39 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' U C 58 " pdb=" C3' U C 58 " pdb=" C2' U C 58 " pdb=" C1' U C 58 " ideal model delta sinusoidal sigma weight residual 36.35 -37.33 73.67 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' A D 56 " pdb=" C3' A D 56 " pdb=" C2' A D 56 " pdb=" C1' A D 56 " ideal model delta sinusoidal sigma weight residual 36.34 -36.96 73.30 1 3.10e+00 1.04e-01 7.12e+02 ... (remaining 11227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2521 0.069 - 0.138: 404 0.138 - 0.207: 49 0.207 - 0.275: 155 0.275 - 0.344: 11 Chirality restraints: 3140 Sorted by residual: chirality pdb=" P U D 57 " pdb=" OP1 U D 57 " pdb=" OP2 U D 57 " pdb=" O5' U D 57 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" P C D 30 " pdb=" OP1 C D 30 " pdb=" OP2 C D 30 " pdb=" O5' C D 30 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" P A D 9 " pdb=" OP1 A D 9 " pdb=" OP2 A D 9 " pdb=" O5' A D 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3137 not shown) Planarity restraints: 2916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO A 638 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 962 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA A 962 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 962 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 963 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 57 " 0.028 2.00e-02 2.50e+03 1.51e-02 5.13e+00 pdb=" N1 U D 57 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U D 57 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U D 57 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U D 57 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U D 57 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U D 57 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U D 57 " -0.006 2.00e-02 2.50e+03 ... (remaining 2913 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2385 2.74 - 3.28: 17750 3.28 - 3.82: 30270 3.82 - 4.36: 35111 4.36 - 4.90: 57511 Nonbonded interactions: 143027 Sorted by model distance: nonbonded pdb=" OG1 THR B 855 " pdb=" OP1 G C 69 " model vdw 2.204 3.040 nonbonded pdb=" O LYS A1040 " pdb=" ND2 ASN A1043 " model vdw 2.205 3.120 nonbonded pdb=" NH1 ARG A 724 " pdb=" O ALA A 772 " model vdw 2.210 3.120 nonbonded pdb=" O PHE B 950 " pdb=" OG1 THR B 953 " model vdw 2.219 3.040 nonbonded pdb=" O VAL A1041 " pdb=" NH1 ARG A1045 " model vdw 2.229 3.120 ... (remaining 143022 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 70 and (name CA or name C or name O or name CB or name OG \ )) or resid 71 through 174 or (resid 175 and (name N or name CA or name C or na \ me O or name CB )) or resid 176 through 446 or (resid 447 through 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 and (n \ ame N or name CA or name C or name O or name CB )) or resid 452 through 939 or r \ esid 941 through 944 or (resid 945 and (name N or name CA or name C or name O or \ name CB )) or resid 946 through 1068)) selection = (chain 'B' and (resid 70 through 493 or (resid 494 and (name N or name CA or nam \ e C or name O or name CB )) or resid 495 through 939 or resid 941 through 972 or \ (resid 973 through 975 and (name N or name CA or name C or name O or name CB )) \ or resid 976 through 978 or (resid 979 through 983 and (name N or name CA or na \ me C or name O or name CB )) or resid 984 through 986 or (resid 987 through 990 \ and (name N or name CA or name C or name O or name CB )) or resid 991 through 10 \ 36 or (resid 1037 through 1040 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1041 through 1047 or (resid 1048 and (name N or name CA or name \ C or name O or name CB )) or resid 1049 through 1068)) } ncs_group { reference = (chain 'C' and resid 1 through 71) selection = chain 'D' } 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=0.50 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: 4.990 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.060 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.008 0.173 19157 Z= 0.394 Angle : 0.885 14.356 26677 Z= 0.462 Chirality : 0.074 0.344 3140 Planarity : 0.005 0.071 2916 Dihedral : 16.554 178.441 7536 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.42 % Allowed : 14.06 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -3.24 (0.18), residues: 1964 helix: -1.92 (0.17), residues: 860 sheet: -1.19 (0.37), residues: 217 loop : -2.58 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 432 TYR 0.019 0.002 TYR A 584 PHE 0.024 0.002 PHE A1014 TRP 0.012 0.002 TRP A 298 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.39 (19155) covalent geometry : angle 0.88492 / 0.46 (26677) hydrogen bonds : bond 0.16677 / 11.13 ( 619) hydrogen bonds : angle 6.65477 / 4.73 ( 1660) Misc. bond : bond 0.02940 / 1.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 164 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8344 (tp) REVERT: B 267 MET cc_start: 0.9143 (mmm) cc_final: 0.8845 (mmp) REVERT: B 420 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7740 (tp) REVERT: B 488 ARG cc_start: 0.9098 (ttt180) cc_final: 0.8852 (tmm-80) REVERT: B 549 ASP cc_start: 0.9191 (t0) cc_final: 0.8939 (m-30) REVERT: B 563 ASN cc_start: 0.8434 (p0) cc_final: 0.7835 (p0) REVERT: B 659 MET cc_start: 0.8445 (mtt) cc_final: 0.8211 (ttm) REVERT: B 743 MET cc_start: 0.9420 (mmt) cc_final: 0.8359 (mmp) REVERT: B 768 LYS cc_start: 0.9560 (mtpp) cc_final: 0.9327 (mmtt) REVERT: B 775 MET cc_start: 0.9049 (tmm) cc_final: 0.7940 (ttt) REVERT: B 875 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8364 (t0) REVERT: B 947 MET cc_start: 0.9160 (tmm) cc_final: 0.8932 (tpt) REVERT: B 1034 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8446 (m) REVERT: A 81 LEU cc_start: 0.9517 (mt) cc_final: 0.9193 (tp) REVERT: A 202 MET cc_start: 0.9393 (ttp) cc_final: 0.9019 (tmm) REVERT: A 264 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: A 420 LEU cc_start: 0.9162 (mt) cc_final: 0.8865 (mm) REVERT: A 441 LEU cc_start: 0.9649 (tp) cc_final: 0.9351 (tp) REVERT: A 528 MET cc_start: 0.9368 (mtp) cc_final: 0.8942 (mtp) REVERT: A 659 MET cc_start: 0.8913 (mtm) cc_final: 0.8395 (ttm) REVERT: A 677 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8712 (tt) REVERT: A 701 LEU cc_start: 0.9132 (pp) cc_final: 0.8828 (tp) REVERT: A 714 MET cc_start: 0.9614 (ttp) cc_final: 0.9231 (ptp) REVERT: A 739 MET cc_start: 0.8753 (mmm) cc_final: 0.7985 (tpp) REVERT: A 743 MET cc_start: 0.9499 (mmm) cc_final: 0.8830 (mmm) REVERT: A 833 LEU cc_start: 0.9164 (mt) cc_final: 0.8630 (pt) REVERT: A 846 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: A 947 MET cc_start: 0.8739 (ttt) cc_final: 0.8399 (ttp) outliers start: 73 outliers final: 7 residues processed: 229 average time/residue: 0.1259 time to fit residues: 45.4382 Evaluate side-chains 103 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN B 631 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 145 HIS A 147 GLN A 177 HIS A 185 ASN A 214 GLN A 442 ASN A 547 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 856 ASN A 870 GLN A1031 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.040244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.030098 restraints weight = 226708.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.030902 restraints weight = 143796.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.031473 restraints weight = 102291.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.031882 restraints weight = 78735.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.032182 restraints weight = 64219.558| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19157 Z= 0.221 Angle : 0.959 19.225 26677 Z= 0.425 Chirality : 0.071 1.048 3140 Planarity : 0.005 0.072 2916 Dihedral : 14.501 169.298 3861 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 0.12 % Allowed : 2.12 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.50 (0.18), residues: 1964 helix: -1.32 (0.17), residues: 875 sheet: -1.04 (0.37), residues: 205 loop : -2.10 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 426 TYR 0.029 0.002 TYR A 123 PHE 0.020 0.002 PHE A 986 TRP 0.026 0.002 TRP A 530 HIS 0.005 0.002 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (19155) covalent geometry : angle 0.95874 / 0.43 (26677) hydrogen bonds : bond 0.04582 / 3.01 ( 619) hydrogen bonds : angle 4.58344 / 3.21 ( 1660) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9040 (ptp) cc_final: 0.8726 (pmm) REVERT: B 202 MET cc_start: 0.9188 (ppp) cc_final: 0.8782 (ppp) REVERT: B 205 MET cc_start: 0.9135 (tpp) cc_final: 0.8787 (tpp) REVERT: B 267 MET cc_start: 0.9251 (mmm) cc_final: 0.8981 (mmm) REVERT: B 549 ASP cc_start: 0.9198 (t0) cc_final: 0.8852 (m-30) REVERT: B 659 MET cc_start: 0.8972 (mtt) cc_final: 0.8378 (ttm) REVERT: B 743 MET cc_start: 0.9631 (mmp) cc_final: 0.9082 (mmp) REVERT: B 775 MET cc_start: 0.8895 (tmm) cc_final: 0.8356 (ptm) REVERT: A 202 MET cc_start: 0.9510 (ttp) cc_final: 0.9033 (tmm) REVERT: A 237 MET cc_start: 0.9132 (ptp) cc_final: 0.8928 (ptt) REVERT: A 441 LEU cc_start: 0.9460 (tp) cc_final: 0.9238 (tp) REVERT: A 637 MET cc_start: 0.8848 (mmp) cc_final: 0.8628 (mmt) REVERT: A 659 MET cc_start: 0.9161 (mtm) cc_final: 0.8617 (ttm) REVERT: A 701 LEU cc_start: 0.9526 (pp) cc_final: 0.9145 (tp) REVERT: A 714 MET cc_start: 0.9524 (ttp) cc_final: 0.9205 (ptp) REVERT: A 739 MET cc_start: 0.8628 (mmm) cc_final: 0.8153 (tpp) REVERT: A 743 MET cc_start: 0.9567 (mmm) cc_final: 0.8964 (mmp) REVERT: A 759 ILE cc_start: 0.8284 (mp) cc_final: 0.7985 (tp) REVERT: A 775 MET cc_start: 0.9255 (tpp) cc_final: 0.8924 (tpp) REVERT: A 947 MET cc_start: 0.8597 (ttt) cc_final: 0.8322 (ttm) REVERT: A 1035 MET cc_start: 0.9405 (mmp) cc_final: 0.9198 (mmt) outliers start: 2 outliers final: 0 residues processed: 100 average time/residue: 0.1224 time to fit residues: 19.7206 Evaluate side-chains 64 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 875 ASN A 82 GLN A 138 ASN A 214 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.038923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.028882 restraints weight = 231698.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.029660 restraints weight = 144854.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.030206 restraints weight = 102194.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.030594 restraints weight = 78313.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.030854 restraints weight = 63757.147| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19157 Z= 0.156 Angle : 0.766 11.341 26677 Z= 0.347 Chirality : 0.056 0.641 3140 Planarity : 0.004 0.056 2916 Dihedral : 14.280 155.027 3861 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.12 % Allowed : 2.18 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.01 (0.18), residues: 1964 helix: -0.86 (0.17), residues: 886 sheet: -1.23 (0.34), residues: 229 loop : -1.77 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1045 TYR 0.014 0.002 TYR B 256 PHE 0.020 0.002 PHE B 824 TRP 0.013 0.001 TRP B 186 HIS 0.008 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (19155) covalent geometry : angle 0.76629 / 0.35 (26677) hydrogen bonds : bond 0.03581 / 2.37 ( 619) hydrogen bonds : angle 4.31184 / 3.02 ( 1660) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 MET cc_start: 0.9331 (mmm) cc_final: 0.9028 (mmm) REVERT: B 549 ASP cc_start: 0.9240 (t0) cc_final: 0.8834 (m-30) REVERT: B 659 MET cc_start: 0.8978 (mtt) cc_final: 0.8344 (ttm) REVERT: B 739 MET cc_start: 0.9039 (tpt) cc_final: 0.8584 (tpp) REVERT: B 743 MET cc_start: 0.9450 (mmp) cc_final: 0.8943 (mmt) REVERT: B 763 MET cc_start: 0.9102 (tpp) cc_final: 0.8707 (mtm) REVERT: B 842 LEU cc_start: 0.9608 (mt) cc_final: 0.9188 (pp) REVERT: B 947 MET cc_start: 0.8963 (tmm) cc_final: 0.8739 (tmm) REVERT: A 202 MET cc_start: 0.9416 (ttp) cc_final: 0.8959 (tmm) REVERT: A 205 MET cc_start: 0.9148 (tpt) cc_final: 0.8759 (tpp) REVERT: A 214 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8474 (mm-40) REVERT: A 237 MET cc_start: 0.9043 (ptp) cc_final: 0.8774 (ptt) REVERT: A 441 LEU cc_start: 0.9489 (tp) cc_final: 0.9196 (tp) REVERT: A 701 LEU cc_start: 0.9636 (pp) cc_final: 0.9403 (tp) REVERT: A 714 MET cc_start: 0.9555 (ttp) cc_final: 0.9272 (ptp) REVERT: A 739 MET cc_start: 0.8584 (mmm) cc_final: 0.8111 (tpp) REVERT: A 743 MET cc_start: 0.9507 (mmm) cc_final: 0.8956 (mmm) REVERT: A 775 MET cc_start: 0.9188 (tpp) cc_final: 0.8747 (tpp) REVERT: A 947 MET cc_start: 0.8732 (ttt) cc_final: 0.7880 (tpp) REVERT: A 1035 MET cc_start: 0.9420 (mmp) cc_final: 0.9216 (mmt) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.1148 time to fit residues: 14.4729 Evaluate side-chains 60 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 201 optimal weight: 6.9990 chunk 197 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 168 optimal weight: 0.1980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN A 138 ASN A 214 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 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 = 0.3288 r_free = 0.3288 target = 0.039357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.029321 restraints weight = 229739.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.030122 restraints weight = 142394.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.030683 restraints weight = 100111.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.031076 restraints weight = 76386.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.031350 restraints weight = 62158.949| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19157 Z= 0.104 Angle : 0.689 11.741 26677 Z= 0.307 Chirality : 0.054 0.498 3140 Planarity : 0.004 0.057 2916 Dihedral : 13.947 157.490 3861 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.06 % Allowed : 1.33 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.62 (0.19), residues: 1964 helix: -0.56 (0.18), residues: 892 sheet: -0.99 (0.36), residues: 218 loop : -1.56 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 426 TYR 0.015 0.001 TYR A 84 PHE 0.015 0.001 PHE A 986 TRP 0.008 0.001 TRP B 119 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (19155) covalent geometry : angle 0.68851 / 0.31 (26677) hydrogen bonds : bond 0.02925 / 1.94 ( 619) hydrogen bonds : angle 3.99524 / 2.80 ( 1660) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9020 (ptp) cc_final: 0.8648 (pmm) REVERT: B 267 MET cc_start: 0.9337 (mmm) cc_final: 0.9027 (mmm) REVERT: B 549 ASP cc_start: 0.9194 (t0) cc_final: 0.8811 (m-30) REVERT: B 659 MET cc_start: 0.8891 (mtt) cc_final: 0.8283 (ttm) REVERT: B 763 MET cc_start: 0.9078 (tpp) cc_final: 0.8811 (mtm) REVERT: B 775 MET cc_start: 0.8636 (tmm) cc_final: 0.7736 (ppp) REVERT: B 842 LEU cc_start: 0.9586 (mt) cc_final: 0.9170 (pp) REVERT: A 202 MET cc_start: 0.9388 (ttp) cc_final: 0.8832 (tmm) REVERT: A 205 MET cc_start: 0.9172 (tpt) cc_final: 0.8654 (tpp) REVERT: A 237 MET cc_start: 0.9030 (ptp) cc_final: 0.8804 (ptt) REVERT: A 267 MET cc_start: 0.9097 (mmp) cc_final: 0.8572 (mmp) REVERT: A 441 LEU cc_start: 0.9466 (tp) cc_final: 0.9169 (tp) REVERT: A 659 MET cc_start: 0.8977 (ttm) cc_final: 0.8065 (ttm) REVERT: A 714 MET cc_start: 0.9540 (ttp) cc_final: 0.9277 (ptp) REVERT: A 739 MET cc_start: 0.8543 (mmm) cc_final: 0.8155 (tpp) REVERT: A 743 MET cc_start: 0.9498 (mmm) cc_final: 0.9159 (mmm) REVERT: A 775 MET cc_start: 0.9087 (tpp) cc_final: 0.8687 (tpp) REVERT: A 833 LEU cc_start: 0.8962 (mm) cc_final: 0.8506 (pt) REVERT: A 947 MET cc_start: 0.8762 (ttt) cc_final: 0.7935 (tpp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1169 time to fit residues: 14.2262 Evaluate side-chains 60 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 64 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 161 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN B 875 ASN A 138 ASN A 214 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.039495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029485 restraints weight = 228289.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.030285 restraints weight = 142062.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030844 restraints weight = 99934.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.031236 restraints weight = 76370.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.031506 restraints weight = 62223.502| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19157 Z= 0.100 Angle : 0.662 11.103 26677 Z= 0.293 Chirality : 0.052 0.362 3140 Planarity : 0.004 0.058 2916 Dihedral : 13.692 177.226 3861 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.06 % Allowed : 1.15 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.16 (0.19), residues: 1964 helix: -0.24 (0.18), residues: 903 sheet: -0.74 (0.37), residues: 221 loop : -1.25 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 426 TYR 0.013 0.001 TYR A 84 PHE 0.014 0.001 PHE A 986 TRP 0.010 0.001 TRP B 119 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (19155) covalent geometry : angle 0.66155 / 0.29 (26677) hydrogen bonds : bond 0.02692 / 1.76 ( 619) hydrogen bonds : angle 3.77682 / 2.63 ( 1660) Misc. bond : bond 0.00058 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8948 (ptp) cc_final: 0.8518 (pmm) REVERT: B 237 MET cc_start: 0.9381 (ptp) cc_final: 0.9011 (ptp) REVERT: B 267 MET cc_start: 0.9353 (mmm) cc_final: 0.9029 (mmm) REVERT: B 549 ASP cc_start: 0.9131 (t0) cc_final: 0.8787 (m-30) REVERT: B 659 MET cc_start: 0.8838 (mtt) cc_final: 0.8207 (ttm) REVERT: B 739 MET cc_start: 0.9079 (tpt) cc_final: 0.8814 (tpp) REVERT: B 743 MET cc_start: 0.9633 (mmp) cc_final: 0.9097 (mmm) REVERT: B 763 MET cc_start: 0.9041 (tpp) cc_final: 0.8824 (mtm) REVERT: B 842 LEU cc_start: 0.9591 (mt) cc_final: 0.9185 (pp) REVERT: A 202 MET cc_start: 0.9395 (ttp) cc_final: 0.9089 (tmm) REVERT: A 205 MET cc_start: 0.9187 (tpt) cc_final: 0.8888 (tpp) REVERT: A 441 LEU cc_start: 0.9438 (tp) cc_final: 0.9139 (tp) REVERT: A 446 MET cc_start: 0.8823 (mpp) cc_final: 0.8064 (tpp) REVERT: A 659 MET cc_start: 0.8976 (ttm) cc_final: 0.8676 (ttm) REVERT: A 714 MET cc_start: 0.9525 (ttp) cc_final: 0.9295 (ptp) REVERT: A 743 MET cc_start: 0.9496 (mmm) cc_final: 0.9271 (mmm) REVERT: A 759 ILE cc_start: 0.8223 (mp) cc_final: 0.7868 (tp) REVERT: A 775 MET cc_start: 0.9041 (tpp) cc_final: 0.8652 (tpp) REVERT: A 833 LEU cc_start: 0.8892 (mm) cc_final: 0.8499 (pt) REVERT: A 947 MET cc_start: 0.8807 (ttt) cc_final: 0.8022 (tpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1216 time to fit residues: 15.0360 Evaluate side-chains 61 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 0.0070 chunk 156 optimal weight: 0.1980 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 79 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 ASN B 875 ASN A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.039305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029375 restraints weight = 228420.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.030170 restraints weight = 141921.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.030725 restraints weight = 99814.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.031109 restraints weight = 76303.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.031399 restraints weight = 62303.099| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19157 Z= 0.093 Angle : 0.653 11.120 26677 Z= 0.288 Chirality : 0.052 0.375 3140 Planarity : 0.004 0.058 2916 Dihedral : 13.610 178.870 3861 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.90 (0.19), residues: 1964 helix: 0.04 (0.18), residues: 893 sheet: -0.62 (0.37), residues: 219 loop : -1.19 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 426 TYR 0.012 0.001 TYR B 256 PHE 0.010 0.001 PHE A 986 TRP 0.008 0.001 TRP B 542 HIS 0.003 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (19155) covalent geometry : angle 0.65317 / 0.29 (26677) hydrogen bonds : bond 0.02643 / 1.74 ( 619) hydrogen bonds : angle 3.66373 / 2.54 ( 1660) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8941 (ptp) cc_final: 0.8492 (pmm) REVERT: B 267 MET cc_start: 0.9364 (mmm) cc_final: 0.9039 (mmm) REVERT: B 549 ASP cc_start: 0.9114 (t0) cc_final: 0.8770 (m-30) REVERT: B 659 MET cc_start: 0.8827 (mtt) cc_final: 0.8214 (ttm) REVERT: B 739 MET cc_start: 0.9053 (tpt) cc_final: 0.8705 (tpp) REVERT: B 743 MET cc_start: 0.9577 (mmp) cc_final: 0.8889 (mmm) REVERT: B 842 LEU cc_start: 0.9595 (mt) cc_final: 0.9186 (pp) REVERT: A 202 MET cc_start: 0.9401 (ttp) cc_final: 0.9093 (tmm) REVERT: A 205 MET cc_start: 0.9205 (tpt) cc_final: 0.8935 (tpp) REVERT: A 441 LEU cc_start: 0.9411 (tp) cc_final: 0.9113 (tp) REVERT: A 446 MET cc_start: 0.8824 (mpp) cc_final: 0.8064 (tpp) REVERT: A 637 MET cc_start: 0.8828 (mpp) cc_final: 0.8400 (mpp) REVERT: A 714 MET cc_start: 0.9526 (ttp) cc_final: 0.9290 (ptp) REVERT: A 739 MET cc_start: 0.8645 (tpt) cc_final: 0.7437 (tpt) REVERT: A 743 MET cc_start: 0.9430 (mmm) cc_final: 0.8542 (mmm) REVERT: A 759 ILE cc_start: 0.8254 (mp) cc_final: 0.7979 (tp) REVERT: A 763 MET cc_start: 0.8153 (ttt) cc_final: 0.7510 (tpt) REVERT: A 947 MET cc_start: 0.8835 (ttt) cc_final: 0.8061 (tpp) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.1171 time to fit residues: 14.2569 Evaluate side-chains 61 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 97 ASN B 875 ASN A 138 ASN A 760 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.036734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.026811 restraints weight = 236653.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.027541 restraints weight = 146404.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028061 restraints weight = 103165.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.028425 restraints weight = 78984.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.028667 restraints weight = 64494.128| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19157 Z= 0.139 Angle : 0.698 10.491 26677 Z= 0.316 Chirality : 0.051 0.381 3140 Planarity : 0.004 0.057 2916 Dihedral : 13.604 172.601 3861 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.06 % Allowed : 0.85 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.90 (0.19), residues: 1964 helix: 0.16 (0.18), residues: 897 sheet: -0.85 (0.37), residues: 210 loop : -1.28 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 694 TYR 0.017 0.002 TYR A 360 PHE 0.012 0.001 PHE B 536 TRP 0.017 0.002 TRP B 186 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (19155) covalent geometry : angle 0.69759 / 0.32 (26677) hydrogen bonds : bond 0.03352 / 2.21 ( 619) hydrogen bonds : angle 3.85265 / 2.67 ( 1660) Misc. bond : bond 0.00089 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8968 (ptp) cc_final: 0.8501 (pmm) REVERT: B 237 MET cc_start: 0.9541 (ptp) cc_final: 0.8744 (ttp) REVERT: B 267 MET cc_start: 0.9380 (mmm) cc_final: 0.8989 (mmm) REVERT: B 549 ASP cc_start: 0.9232 (t0) cc_final: 0.8922 (m-30) REVERT: B 659 MET cc_start: 0.9148 (mtt) cc_final: 0.8379 (ttm) REVERT: B 739 MET cc_start: 0.9089 (tpt) cc_final: 0.8626 (tpp) REVERT: B 743 MET cc_start: 0.9633 (mmp) cc_final: 0.8965 (mmt) REVERT: B 763 MET cc_start: 0.8636 (mpp) cc_final: 0.8341 (mpp) REVERT: B 842 LEU cc_start: 0.9626 (mt) cc_final: 0.9224 (pp) REVERT: A 202 MET cc_start: 0.9422 (ttp) cc_final: 0.8898 (tmm) REVERT: A 441 LEU cc_start: 0.9396 (tp) cc_final: 0.9064 (tp) REVERT: A 446 MET cc_start: 0.8936 (mpp) cc_final: 0.8320 (tpp) REVERT: A 637 MET cc_start: 0.8889 (mpp) cc_final: 0.8555 (mpp) REVERT: A 714 MET cc_start: 0.9549 (ttp) cc_final: 0.9269 (ptp) REVERT: A 739 MET cc_start: 0.8622 (tpt) cc_final: 0.8330 (tpt) REVERT: A 759 ILE cc_start: 0.8580 (mp) cc_final: 0.8243 (tp) REVERT: A 775 MET cc_start: 0.9284 (tpp) cc_final: 0.8974 (tpp) REVERT: A 947 MET cc_start: 0.8848 (ttt) cc_final: 0.8194 (tpp) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1027 time to fit residues: 11.0981 Evaluate side-chains 56 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 194 optimal weight: 50.0000 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 177 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 182 optimal weight: 0.2980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 97 ASN B 875 ASN A 138 ASN ** A 760 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 = 0.3197 r_free = 0.3197 target = 0.036583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.026727 restraints weight = 233611.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.027466 restraints weight = 142914.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027978 restraints weight = 100175.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028339 restraints weight = 76592.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.028597 restraints weight = 62504.882| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19157 Z= 0.113 Angle : 0.656 10.428 26677 Z= 0.293 Chirality : 0.051 0.380 3140 Planarity : 0.004 0.055 2916 Dihedral : 13.610 170.480 3861 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.06 % Allowed : 0.61 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1964 helix: 0.34 (0.18), residues: 904 sheet: -0.73 (0.36), residues: 209 loop : -1.21 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1045 TYR 0.012 0.001 TYR B 212 PHE 0.009 0.001 PHE B 284 TRP 0.010 0.001 TRP A 186 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (19155) covalent geometry : angle 0.65639 / 0.29 (26677) hydrogen bonds : bond 0.02874 / 1.88 ( 619) hydrogen bonds : angle 3.76096 / 2.62 ( 1660) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 MET cc_start: 0.9571 (ptp) cc_final: 0.8637 (ttp) REVERT: B 267 MET cc_start: 0.9404 (mmm) cc_final: 0.9128 (mmp) REVERT: B 549 ASP cc_start: 0.9189 (t0) cc_final: 0.8885 (m-30) REVERT: B 659 MET cc_start: 0.9060 (mtt) cc_final: 0.8425 (ttm) REVERT: B 739 MET cc_start: 0.9103 (tpt) cc_final: 0.8704 (tpp) REVERT: B 743 MET cc_start: 0.9641 (mmp) cc_final: 0.8865 (mmp) REVERT: B 763 MET cc_start: 0.8424 (mpp) cc_final: 0.7999 (mpp) REVERT: B 775 MET cc_start: 0.8619 (tmm) cc_final: 0.7957 (ppp) REVERT: B 842 LEU cc_start: 0.9641 (mt) cc_final: 0.9247 (pp) REVERT: A 202 MET cc_start: 0.9354 (ttp) cc_final: 0.9106 (tmm) REVERT: A 237 MET cc_start: 0.9215 (ptp) cc_final: 0.8985 (ptt) REVERT: A 441 LEU cc_start: 0.9441 (tp) cc_final: 0.9138 (tp) REVERT: A 446 MET cc_start: 0.8905 (mpp) cc_final: 0.8353 (tpp) REVERT: A 637 MET cc_start: 0.8901 (mpp) cc_final: 0.8563 (mpp) REVERT: A 659 MET cc_start: 0.8988 (ttt) cc_final: 0.7856 (ttp) REVERT: A 714 MET cc_start: 0.9542 (ttp) cc_final: 0.9249 (ptp) REVERT: A 739 MET cc_start: 0.8694 (tpt) cc_final: 0.7629 (tpt) REVERT: A 743 MET cc_start: 0.9535 (mmm) cc_final: 0.8411 (mmm) REVERT: A 759 ILE cc_start: 0.8489 (mp) cc_final: 0.8189 (tp) REVERT: A 763 MET cc_start: 0.8412 (ttt) cc_final: 0.7873 (tpt) REVERT: A 947 MET cc_start: 0.8953 (ttt) cc_final: 0.8422 (tpp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1027 time to fit residues: 10.7279 Evaluate side-chains 57 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 97 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 149 GLN A 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.034914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.025162 restraints weight = 241713.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.025872 restraints weight = 146388.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.026355 restraints weight = 101214.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.026695 restraints weight = 77053.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.026938 restraints weight = 62715.896| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19157 Z= 0.170 Angle : 0.736 10.966 26677 Z= 0.337 Chirality : 0.052 0.376 3140 Planarity : 0.005 0.051 2916 Dihedral : 13.682 165.161 3861 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.80 (0.19), residues: 1964 helix: 0.32 (0.17), residues: 893 sheet: -0.93 (0.35), residues: 222 loop : -1.28 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1045 TYR 0.019 0.002 TYR A 360 PHE 0.014 0.002 PHE B 536 TRP 0.018 0.002 TRP B 186 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (19155) covalent geometry : angle 0.73558 / 0.34 (26677) hydrogen bonds : bond 0.03749 / 2.44 ( 619) hydrogen bonds : angle 4.04035 / 2.80 ( 1660) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 MET cc_start: 0.9614 (ptp) cc_final: 0.8909 (ttp) REVERT: B 267 MET cc_start: 0.9498 (mmm) cc_final: 0.9171 (mmp) REVERT: B 549 ASP cc_start: 0.9196 (t0) cc_final: 0.8846 (m-30) REVERT: B 637 MET cc_start: 0.9451 (mmp) cc_final: 0.9235 (mmm) REVERT: B 659 MET cc_start: 0.9239 (mtt) cc_final: 0.8436 (ttm) REVERT: B 739 MET cc_start: 0.9127 (tpt) cc_final: 0.8730 (tpp) REVERT: B 743 MET cc_start: 0.9671 (mmp) cc_final: 0.8965 (mmm) REVERT: B 763 MET cc_start: 0.8532 (mpp) cc_final: 0.7983 (mpp) REVERT: B 775 MET cc_start: 0.8812 (tmm) cc_final: 0.8454 (tmm) REVERT: B 842 LEU cc_start: 0.9686 (mt) cc_final: 0.9302 (pp) REVERT: A 202 MET cc_start: 0.9354 (ttp) cc_final: 0.9119 (ppp) REVERT: A 441 LEU cc_start: 0.9419 (tp) cc_final: 0.9067 (tp) REVERT: A 446 MET cc_start: 0.8891 (mpp) cc_final: 0.8410 (tpp) REVERT: A 637 MET cc_start: 0.8921 (mpp) cc_final: 0.8690 (mpp) REVERT: A 659 MET cc_start: 0.9071 (ttt) cc_final: 0.8112 (ttt) REVERT: A 714 MET cc_start: 0.9562 (ttp) cc_final: 0.9260 (ptp) REVERT: A 739 MET cc_start: 0.8716 (tpt) cc_final: 0.7713 (tpt) REVERT: A 743 MET cc_start: 0.9523 (mmm) cc_final: 0.8540 (mmm) REVERT: A 947 MET cc_start: 0.9132 (ttt) cc_final: 0.8673 (tpp) REVERT: A 1035 MET cc_start: 0.9306 (mmp) cc_final: 0.9068 (mmm) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0966 time to fit residues: 10.2944 Evaluate side-chains 56 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 144 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 7 optimal weight: 0.0870 chunk 132 optimal weight: 6.9990 chunk 196 optimal weight: 0.0020 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 97 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.035944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.026155 restraints weight = 236330.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026893 restraints weight = 141909.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.027411 restraints weight = 98140.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.027768 restraints weight = 74329.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028020 restraints weight = 60331.541| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19157 Z= 0.098 Angle : 0.661 10.258 26677 Z= 0.294 Chirality : 0.051 0.370 3140 Planarity : 0.004 0.053 2916 Dihedral : 13.600 167.326 3861 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.51 (0.19), residues: 1964 helix: 0.53 (0.18), residues: 903 sheet: -0.61 (0.37), residues: 205 loop : -1.16 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.012 0.001 TYR A 84 PHE 0.009 0.001 PHE A 986 TRP 0.010 0.001 TRP A 85 HIS 0.005 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (19155) covalent geometry : angle 0.66103 / 0.29 (26677) hydrogen bonds : bond 0.02760 / 1.79 ( 619) hydrogen bonds : angle 3.74374 / 2.60 ( 1660) Misc. bond : bond 0.00058 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 MET cc_start: 0.9613 (ptp) cc_final: 0.8893 (ttp) REVERT: B 267 MET cc_start: 0.9506 (mmm) cc_final: 0.9222 (mmp) REVERT: B 549 ASP cc_start: 0.9169 (t0) cc_final: 0.8863 (m-30) REVERT: B 659 MET cc_start: 0.9054 (mtt) cc_final: 0.8407 (ttm) REVERT: B 739 MET cc_start: 0.9111 (tpt) cc_final: 0.8677 (tpp) REVERT: B 743 MET cc_start: 0.9665 (mmp) cc_final: 0.8860 (mmp) REVERT: B 763 MET cc_start: 0.8462 (mpp) cc_final: 0.7949 (mpp) REVERT: B 775 MET cc_start: 0.8669 (tmm) cc_final: 0.7935 (ppp) REVERT: B 842 LEU cc_start: 0.9686 (mt) cc_final: 0.9280 (pp) REVERT: A 237 MET cc_start: 0.9207 (ptp) cc_final: 0.8958 (ptm) REVERT: A 441 LEU cc_start: 0.9412 (tp) cc_final: 0.9097 (tp) REVERT: A 446 MET cc_start: 0.8902 (mpp) cc_final: 0.8451 (tpp) REVERT: A 659 MET cc_start: 0.9001 (ttt) cc_final: 0.8062 (ttt) REVERT: A 714 MET cc_start: 0.9532 (ttp) cc_final: 0.9222 (ptp) REVERT: A 739 MET cc_start: 0.8687 (tpt) cc_final: 0.7655 (tpt) REVERT: A 743 MET cc_start: 0.9522 (mmm) cc_final: 0.8540 (mmm) REVERT: A 947 MET cc_start: 0.9156 (ttt) cc_final: 0.8614 (tpp) REVERT: A 1035 MET cc_start: 0.9275 (mmp) cc_final: 0.9047 (mmm) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1112 time to fit residues: 11.9382 Evaluate side-chains 56 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0270 chunk 71 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 97 ASN B 215 GLN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 160 GLN A 570 ASN A 663 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.026401 restraints weight = 235619.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.027167 restraints weight = 141135.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027683 restraints weight = 97012.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028041 restraints weight = 73300.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028280 restraints weight = 59553.865| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19157 Z= 0.095 Angle : 0.654 9.932 26677 Z= 0.288 Chirality : 0.050 0.363 3140 Planarity : 0.004 0.052 2916 Dihedral : 13.458 168.815 3861 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.12 % Allowed : 0.30 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.31 (0.20), residues: 1964 helix: 0.68 (0.18), residues: 893 sheet: -0.42 (0.37), residues: 203 loop : -1.05 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 426 TYR 0.010 0.001 TYR B 212 PHE 0.009 0.001 PHE B 284 TRP 0.008 0.001 TRP B 119 HIS 0.003 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (19155) covalent geometry : angle 0.65354 / 0.29 (26677) hydrogen bonds : bond 0.02655 / 1.70 ( 619) hydrogen bonds : angle 3.62596 / 2.52 ( 1660) Misc. bond : bond 0.00064 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2833.89 seconds wall clock time: 49 minutes 38.26 seconds (2978.26 seconds total)