Starting phenix.real_space_refine on Sat Sep 12 22:28:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk1_33240/09_2026/7xk1_33240.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 150 5.49 5 S 62 5.16 5 C 11236 2.51 5 N 3188 2.21 5 O 3916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7711 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 non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 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, 7711 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 non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 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: 7862 Chain: "B" 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 B 1 " pdbres=" C B 2 " Chain: "C" Number of atoms: 7716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7711 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 non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 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, 7711 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 non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 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: 7862 Chain: "D" 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 D 1 " pdbres=" C D 2 " Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 residue: pdb=" N AALA C 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA C 940 " occ=0.50 Time building chain proxies: 5.87, per 1000 atoms: 0.32 Number of scatterers: 18552 At special positions: 0 Unit cell: (204.6, 169.4, 118.8, 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 150 15.00 O 3916 8.00 N 3188 7.00 C 11236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS C 95 " distance=2.54 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: 1.18 Conformation dependent library (CDL) restraints added in 1.1 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: 3696 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 16 sheets defined 52.0% alpha, 13.1% beta 32 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.814A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TRP A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.996A pdb=" N PHE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 4.123A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.844A pdb=" N GLU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.112A pdb=" N ILE A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.500A pdb=" N ALA A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 352 removed outlier: 4.153A pdb=" N ARG A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.538A pdb=" N LYS A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.637A pdb=" N GLU A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 508 through 521 Proline residue: A 516 - end of helix removed outlier: 3.642A pdb=" N SER A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.573A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.875A pdb=" N HIS A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 610 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 631 removed outlier: 4.119A pdb=" N GLU A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 650 removed outlier: 3.836A pdb=" N PHE A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 650 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 removed outlier: 3.684A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 716 removed outlier: 3.763A pdb=" N VAL A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 700 " --> pdb=" O GLY A 696 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 4.402A pdb=" N LEU A 727 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 728 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 729 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 757 removed outlier: 5.065A pdb=" N ALA A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 763 through 771 removed outlier: 3.664A pdb=" N ILE A 767 " --> pdb=" O MET A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.710A pdb=" N ALA A 779 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 removed outlier: 4.254A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 786' Processing helix chain 'A' and resid 787 through 790 Processing helix chain 'A' and resid 792 through 802 removed outlier: 3.517A pdb=" N GLY A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 removed outlier: 3.735A pdb=" N ALA A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 810 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 848 removed outlier: 3.619A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 874 Processing helix chain 'A' and resid 880 through 891 removed outlier: 4.097A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 917 removed outlier: 4.424A pdb=" N ILE A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.581A pdb=" N SER A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 951 removed outlier: 4.003A pdb=" N GLU A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.753A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 removed outlier: 3.546A pdb=" N ILE A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 971 " --> pdb=" O THR A 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 966 through 971' Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 988 through 1003 removed outlier: 3.906A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.804A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A1027 " --> pdb=" O GLN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1054 Processing helix chain 'C' and resid 73 through 89 removed outlier: 3.815A pdb=" N ILE C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN C 79 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 84 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 133 Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.996A pdb=" N PHE C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 removed outlier: 4.122A pdb=" N LEU C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.748A pdb=" N GLU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS C 274 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 4.110A pdb=" N ILE C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 282 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 321 removed outlier: 3.500A pdb=" N ALA C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 352 removed outlier: 4.154A pdb=" N ARG C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 418 removed outlier: 3.537A pdb=" N LYS C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 410 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.636A pdb=" N GLU C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 508 through 521 Proline residue: C 516 - end of helix removed outlier: 3.643A pdb=" N SER C 520 " --> pdb=" O PRO C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 591 removed outlier: 3.573A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 613 removed outlier: 3.874A pdb=" N HIS C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 610 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 613 " --> pdb=" O SER C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 631 removed outlier: 4.118A pdb=" N GLU C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN C 631 " --> pdb=" O GLN C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 650 removed outlier: 3.835A pdb=" N PHE C 647 " --> pdb=" O ASP C 644 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 649 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 650 " --> pdb=" O PHE C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 662 removed outlier: 3.684A pdb=" N LEU C 655 " --> pdb=" O PRO C 651 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 657 " --> pdb=" O ASP C 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS C 662 " --> pdb=" O VAL C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 716 removed outlier: 3.764A pdb=" N VAL C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C 699 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL C 700 " --> pdb=" O GLY C 696 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 729 removed outlier: 4.404A pdb=" N LEU C 727 " --> pdb=" O ARG C 724 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 728 " --> pdb=" O ASP C 725 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C 729 " --> pdb=" O GLN C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 757 removed outlier: 5.065A pdb=" N ALA C 751 " --> pdb=" O GLU C 747 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 762 No H-bonds generated for 'chain 'C' and resid 760 through 762' Processing helix chain 'C' and resid 763 through 771 removed outlier: 3.662A pdb=" N ILE C 767 " --> pdb=" O MET C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 780 removed outlier: 3.709A pdb=" N ALA C 779 " --> pdb=" O SER C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 786 removed outlier: 4.254A pdb=" N GLU C 785 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 786 " --> pdb=" O ILE C 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 781 through 786' Processing helix chain 'C' and resid 787 through 790 Processing helix chain 'C' and resid 792 through 802 removed outlier: 3.516A pdb=" N GLY C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 removed outlier: 3.735A pdb=" N ALA C 808 " --> pdb=" O SER C 804 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 809 " --> pdb=" O GLU C 805 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 810 " --> pdb=" O GLN C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 848 removed outlier: 3.620A pdb=" N VAL C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 833 " --> pdb=" O PRO C 829 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 848 " --> pdb=" O GLY C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 874 Processing helix chain 'C' and resid 880 through 891 removed outlier: 4.097A pdb=" N THR C 886 " --> pdb=" O THR C 882 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 887 " --> pdb=" O LYS C 883 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 891 " --> pdb=" O LEU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 917 removed outlier: 4.425A pdb=" N ILE C 901 " --> pdb=" O ASP C 897 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 930 removed outlier: 3.580A pdb=" N SER C 928 " --> pdb=" O GLU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 951 removed outlier: 4.004A pdb=" N GLU C 946 " --> pdb=" O GLN C 942 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 948 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 949 " --> pdb=" O ILE C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.754A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 971 removed outlier: 3.545A pdb=" N ILE C 970 " --> pdb=" O PRO C 966 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 971 " --> pdb=" O THR C 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 966 through 971' Processing helix chain 'C' and resid 974 through 978 Processing helix chain 'C' and resid 988 through 1003 removed outlier: 3.906A pdb=" N ARG C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1019 Processing helix chain 'C' and resid 1021 through 1032 removed outlier: 3.803A pdb=" N LEU C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C1027 " --> pdb=" O GLN C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1054 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.803A pdb=" N ALA A 122 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 207 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.583A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.776A pdb=" N LEU A 434 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 390 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 440 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG A 384 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA5, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619 removed outlier: 7.056A pdb=" N PHE A 666 " --> pdb=" O CYS A 679 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS A 679 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL A 668 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 733 removed outlier: 6.322A pdb=" N GLY A 737 " --> pdb=" O PHE A 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.802A pdb=" N ALA C 122 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 207 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET C 202 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 208 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP C 194 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 179 through 183 removed outlier: 6.582A pdb=" N TRP C 194 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 208 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET C 202 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 425 through 430 removed outlier: 3.776A pdb=" N LEU C 434 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 390 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 440 " --> pdb=" O ARG C 384 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG C 384 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AB4, first strand: chain 'C' and resid 555 through 556 Processing sheet with id=AB5, first strand: chain 'C' and resid 564 through 565 Processing sheet with id=AB6, first strand: chain 'C' and resid 617 through 619 removed outlier: 7.056A pdb=" N PHE C 666 " --> pdb=" O CYS C 679 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS C 679 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 668 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET C 637 " --> pdb=" O ALA C 684 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 731 through 733 removed outlier: 6.323A pdb=" N GLY C 737 " --> pdb=" O PHE C 732 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2820 1.31 - 1.44: 5792 1.44 - 1.56: 10216 1.56 - 1.69: 296 1.69 - 1.81: 104 Bond restraints: 19228 Sorted by residual: bond pdb=" C2 GTP D 1 " pdb=" N2 GTP D 1 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" N ILE A 969 " pdb=" CA ILE A 969 " ideal model delta sigma weight residual 1.459 1.505 -0.047 1.28e-02 6.10e+03 1.32e+01 bond pdb=" N THR A 967 " pdb=" CA THR A 967 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N THR C 967 " pdb=" CA THR C 967 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 ... (remaining 19223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 25887 1.83 - 3.66: 757 3.66 - 5.49: 108 5.49 - 7.32: 18 7.32 - 9.15: 12 Bond angle restraints: 26782 Sorted by residual: angle pdb=" N ARG C 965 " pdb=" CA ARG C 965 " pdb=" C ARG C 965 " ideal model delta sigma weight residual 112.75 103.94 8.81 1.36e+00 5.41e-01 4.19e+01 angle pdb=" N ARG A 965 " pdb=" CA ARG A 965 " pdb=" C ARG A 965 " ideal model delta sigma weight residual 112.75 103.97 8.78 1.36e+00 5.41e-01 4.17e+01 angle pdb=" C PRO A 966 " pdb=" CA PRO A 966 " pdb=" CB PRO A 966 " ideal model delta sigma weight residual 112.64 105.71 6.93 1.74e+00 3.30e-01 1.59e+01 angle pdb=" C PRO C 966 " pdb=" CA PRO C 966 " pdb=" CB PRO C 966 " ideal model delta sigma weight residual 112.64 105.74 6.90 1.74e+00 3.30e-01 1.57e+01 angle pdb=" N ASN C 97 " pdb=" CA ASN C 97 " pdb=" C ASN C 97 " ideal model delta sigma weight residual 112.13 106.88 5.25 1.37e+00 5.33e-01 1.47e+01 ... (remaining 26777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.67: 10321 19.67 - 39.35: 673 39.35 - 59.02: 244 59.02 - 78.70: 35 78.70 - 98.37: 8 Dihedral angle restraints: 11281 sinusoidal: 5565 harmonic: 5716 Sorted by residual: dihedral pdb=" C4' G B 17 " pdb=" C3' G B 17 " pdb=" C2' G B 17 " pdb=" C1' G B 17 " ideal model delta sinusoidal sigma weight residual 36.35 -36.59 72.93 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' G D 17 " pdb=" C3' G D 17 " pdb=" C2' G D 17 " pdb=" C1' G D 17 " ideal model delta sinusoidal sigma weight residual 36.35 -36.49 72.83 1 3.10e+00 1.04e-01 7.04e+02 dihedral pdb=" C4' U D 46 " pdb=" C3' U D 46 " pdb=" C2' U D 46 " pdb=" C1' U D 46 " ideal model delta sinusoidal sigma weight residual 36.35 -35.75 72.09 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 11278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2928 0.116 - 0.231: 111 0.231 - 0.347: 113 0.347 - 0.462: 0 0.462 - 0.578: 2 Chirality restraints: 3154 Sorted by residual: chirality pdb=" P G D 33 " pdb=" OP1 G D 33 " pdb=" OP2 G D 33 " pdb=" O5' G D 33 " both_signs ideal model delta sigma weight residual True 2.17 -2.75 -0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" P G D 38 " pdb=" OP1 G D 38 " pdb=" OP2 G D 38 " pdb=" O5' G D 38 " both_signs ideal model delta sigma weight residual True 2.17 -2.73 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" P C D 6 " pdb=" OP1 C D 6 " pdb=" OP2 C D 6 " pdb=" O5' C D 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 3151 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 637 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C 638 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 638 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 638 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 638 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C1063 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C SER C1063 " 0.027 2.00e-02 2.50e+03 pdb=" O SER C1063 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C1064 " -0.009 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2646 2.75 - 3.29: 17800 3.29 - 3.83: 30779 3.83 - 4.36: 34732 4.36 - 4.90: 56894 Nonbonded interactions: 142851 Sorted by model distance: nonbonded pdb=" O PHE C 950 " pdb=" OG1 THR C 953 " model vdw 2.217 3.040 nonbonded pdb=" O PHE A 950 " pdb=" OG1 THR A 953 " model vdw 2.218 3.040 nonbonded pdb=" O GLU C 206 " pdb=" NH1 ARG C 234 " model vdw 2.241 3.120 nonbonded pdb=" O GLU A 206 " pdb=" NH1 ARG A 234 " model vdw 2.241 3.120 nonbonded pdb=" OE1 GLU C 389 " pdb=" OH TYR C 584 " model vdw 2.245 3.040 ... (remaining 142846 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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: 4.700 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 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 : 0.006 0.505 19231 Z= 0.336 Angle : 0.876 58.787 26784 Z= 0.432 Chirality : 0.072 0.578 3154 Planarity : 0.004 0.043 2922 Dihedral : 14.676 98.374 7582 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.07 % Allowed : 8.37 % Favored : 88.55 % 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: -1.21 (0.19), residues: 1964 helix: -0.14 (0.18), residues: 878 sheet: -0.34 (0.37), residues: 238 loop : -1.60 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 694 TYR 0.013 0.001 TYR A 230 PHE 0.010 0.001 PHE A 544 TRP 0.008 0.001 TRP A 194 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.22 (19228) covalent geometry : angle 0.71392 / 0.36 (26782) SS BOND : bond 0.50506 / 26.58 ( 1) SS BOND : angle 58.70788 / 32.77 ( 2) hydrogen bonds : bond 0.16747 / 11.39 ( 737) hydrogen bonds : angle 7.19287 / 5.08 ( 2024) Misc. bond : bond 0.17610 / 8.83 ( 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 445 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 394 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.5538 (m) cc_final: 0.4617 (t) REVERT: A 153 LYS cc_start: 0.4172 (ttpt) cc_final: 0.3517 (tttt) REVERT: A 167 LEU cc_start: 0.8187 (tp) cc_final: 0.7884 (tp) REVERT: A 495 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: A 619 ILE cc_start: 0.9080 (pt) cc_final: 0.8776 (mp) REVERT: A 869 VAL cc_start: 0.9310 (m) cc_final: 0.9058 (p) REVERT: C 254 ILE cc_start: 0.8910 (pt) cc_final: 0.8586 (tp) REVERT: C 280 ILE cc_start: 0.7104 (mm) cc_final: 0.6888 (mm) REVERT: C 305 ASP cc_start: 0.6896 (t70) cc_final: 0.6657 (t70) REVERT: C 341 GLN cc_start: 0.7792 (pt0) cc_final: 0.7129 (tt0) REVERT: C 495 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.4672 (m-80) REVERT: C 655 LEU cc_start: 0.8661 (mt) cc_final: 0.8064 (tt) REVERT: C 741 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7376 (p0) REVERT: C 743 MET cc_start: 0.8721 (mmt) cc_final: 0.8472 (mmp) REVERT: C 775 MET cc_start: 0.8697 (tmm) cc_final: 0.8093 (tmm) REVERT: C 866 TYR cc_start: 0.8390 (t80) cc_final: 0.8162 (t80) outliers start: 51 outliers final: 3 residues processed: 436 average time/residue: 0.1495 time to fit residues: 96.3825 Evaluate side-chains 193 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 10.0000 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 147 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 445 GLN C 97 ASN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 341 GLN C 352 ASN C 660 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.093686 restraints weight = 58497.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096153 restraints weight = 102054.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097066 restraints weight = 48535.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.097456 restraints weight = 34185.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097879 restraints weight = 28736.734| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19231 Z= 0.174 Angle : 0.924 15.248 26784 Z= 0.409 Chirality : 0.071 0.926 3154 Planarity : 0.005 0.047 2922 Dihedral : 13.579 147.507 3884 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 0.06 % Allowed : 1.39 % Favored : 98.55 % 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: -1.20 (0.19), residues: 1964 helix: -0.11 (0.18), residues: 894 sheet: -0.27 (0.35), residues: 226 loop : -1.65 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 702 TYR 0.021 0.002 TYR C 963 PHE 0.031 0.002 PHE C 710 TRP 0.015 0.001 TRP C 198 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (19228) covalent geometry : angle 0.92388 / 0.41 (26782) SS BOND : bond 0.00766 / 0.40 ( 1) SS BOND : angle 3.75926 / 2.12 ( 2) hydrogen bonds : bond 0.04299 / 2.77 ( 737) hydrogen bonds : angle 4.40488 / 3.03 ( 2024) Misc. bond : bond 0.00062 / 0.03 ( 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 235 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8319 (tp) cc_final: 0.7949 (tp) REVERT: A 205 MET cc_start: 0.7027 (ttm) cc_final: 0.6813 (ttp) REVERT: A 314 PHE cc_start: 0.8059 (t80) cc_final: 0.7819 (t80) REVERT: A 352 ASN cc_start: 0.7001 (p0) cc_final: 0.6778 (p0) REVERT: A 389 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 573 LEU cc_start: 0.8324 (tp) cc_final: 0.8055 (tt) REVERT: A 619 ILE cc_start: 0.9072 (pt) cc_final: 0.8735 (mp) REVERT: A 842 LEU cc_start: 0.8551 (pp) cc_final: 0.8317 (pp) REVERT: A 869 VAL cc_start: 0.9123 (m) cc_final: 0.8746 (p) REVERT: C 199 GLU cc_start: 0.7438 (pt0) cc_final: 0.7231 (mt-10) REVERT: C 205 MET cc_start: 0.7068 (mmm) cc_final: 0.6763 (mmm) REVERT: C 280 ILE cc_start: 0.7245 (mm) cc_final: 0.7011 (mm) REVERT: C 305 ASP cc_start: 0.6830 (t70) cc_final: 0.6555 (t70) REVERT: C 341 GLN cc_start: 0.7479 (pt0) cc_final: 0.7182 (tt0) REVERT: C 655 LEU cc_start: 0.8671 (mt) cc_final: 0.8300 (tt) REVERT: C 683 VAL cc_start: 0.8998 (t) cc_final: 0.8775 (m) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1282 time to fit residues: 47.7412 Evaluate side-chains 163 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 173 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 575 ASN A 733 HIS C 76 GLN C 149 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.117747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093933 restraints weight = 57878.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.094062 restraints weight = 89515.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093116 restraints weight = 46922.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.093740 restraints weight = 35218.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.093699 restraints weight = 27766.809| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19231 Z= 0.139 Angle : 0.744 11.878 26784 Z= 0.339 Chirality : 0.056 0.369 3154 Planarity : 0.004 0.053 2922 Dihedral : 13.635 154.867 3884 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.18 % Allowed : 1.75 % Favored : 98.07 % 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: -1.23 (0.18), residues: 1964 helix: -0.19 (0.18), residues: 896 sheet: -0.31 (0.35), residues: 226 loop : -1.59 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 910 TYR 0.019 0.002 TYR A 230 PHE 0.021 0.002 PHE A 210 TRP 0.014 0.001 TRP C 198 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (19228) covalent geometry : angle 0.74382 / 0.34 (26782) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 3.54567 / 1.91 ( 2) hydrogen bonds : bond 0.03634 / 2.37 ( 737) hydrogen bonds : angle 4.25331 / 2.94 ( 2024) Misc. bond : bond 0.00064 / 0.03 ( 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 208 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7638 (mpp) cc_final: 0.7247 (mpt) REVERT: A 183 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 205 MET cc_start: 0.7139 (ttm) cc_final: 0.6895 (ttp) REVERT: A 314 PHE cc_start: 0.8199 (t80) cc_final: 0.7959 (t80) REVERT: A 550 LEU cc_start: 0.7861 (tp) cc_final: 0.7649 (tp) REVERT: A 619 ILE cc_start: 0.9065 (pt) cc_final: 0.8752 (mp) REVERT: A 842 LEU cc_start: 0.8613 (pp) cc_final: 0.8365 (pp) REVERT: A 869 VAL cc_start: 0.9156 (m) cc_final: 0.8711 (p) REVERT: C 205 MET cc_start: 0.7183 (mmm) cc_final: 0.6912 (mmm) REVERT: C 206 GLU cc_start: 0.5952 (tt0) cc_final: 0.5532 (tt0) REVERT: C 237 MET cc_start: 0.8537 (ttm) cc_final: 0.8026 (ttp) REVERT: C 280 ILE cc_start: 0.7047 (mm) cc_final: 0.6816 (mm) REVERT: C 305 ASP cc_start: 0.6734 (t70) cc_final: 0.6448 (t70) REVERT: C 655 LEU cc_start: 0.8773 (mt) cc_final: 0.8339 (tt) outliers start: 3 outliers final: 0 residues processed: 208 average time/residue: 0.1338 time to fit residues: 43.6302 Evaluate side-chains 139 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 171 optimal weight: 0.9980 chunk 148 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 341 GLN A 733 HIS ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.115010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.092022 restraints weight = 57183.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.089791 restraints weight = 80963.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.089117 restraints weight = 54358.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.089392 restraints weight = 56548.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089072 restraints weight = 44223.095| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19231 Z= 0.151 Angle : 0.734 10.303 26784 Z= 0.341 Chirality : 0.053 0.283 3154 Planarity : 0.005 0.056 2922 Dihedral : 13.520 159.429 3884 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % 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: -1.07 (0.19), residues: 1964 helix: -0.02 (0.18), residues: 890 sheet: -0.31 (0.35), residues: 214 loop : -1.50 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 735 TYR 0.024 0.002 TYR A 230 PHE 0.026 0.002 PHE A 210 TRP 0.014 0.002 TRP C 198 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19228) covalent geometry : angle 0.73386 / 0.34 (26782) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 3.62547 / 1.99 ( 2) hydrogen bonds : bond 0.03615 / 2.37 ( 737) hydrogen bonds : angle 4.35376 / 3.01 ( 2024) Misc. bond : bond 0.00046 / 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 176 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7930 (mpp) cc_final: 0.7561 (mpp) REVERT: A 205 MET cc_start: 0.7448 (ttm) cc_final: 0.7136 (ttp) REVERT: A 314 PHE cc_start: 0.8535 (t80) cc_final: 0.8280 (t80) REVERT: A 550 LEU cc_start: 0.7958 (tp) cc_final: 0.7710 (tp) REVERT: A 619 ILE cc_start: 0.9098 (pt) cc_final: 0.8806 (mp) REVERT: C 237 MET cc_start: 0.8649 (ttm) cc_final: 0.8204 (ttp) REVERT: C 655 LEU cc_start: 0.8980 (mt) cc_final: 0.8459 (tt) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1320 time to fit residues: 36.8713 Evaluate side-chains 120 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 10 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 478 ASN A 733 HIS C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.114901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090174 restraints weight = 57207.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.089864 restraints weight = 90806.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088462 restraints weight = 49797.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.088848 restraints weight = 42899.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.089129 restraints weight = 30217.358| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19231 Z= 0.129 Angle : 0.697 9.771 26784 Z= 0.321 Chirality : 0.052 0.284 3154 Planarity : 0.004 0.050 2922 Dihedral : 13.465 161.137 3884 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % 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: -0.88 (0.19), residues: 1964 helix: 0.17 (0.18), residues: 896 sheet: -0.30 (0.36), residues: 214 loop : -1.43 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 724 TYR 0.021 0.002 TYR A 230 PHE 0.020 0.001 PHE A 210 TRP 0.011 0.001 TRP C 530 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19228) covalent geometry : angle 0.69655 / 0.32 (26782) SS BOND : bond 0.00325 / 0.17 ( 1) SS BOND : angle 3.96049 / 2.19 ( 2) hydrogen bonds : bond 0.03369 / 2.20 ( 737) hydrogen bonds : angle 4.20044 / 2.92 ( 2024) Misc. bond : bond 0.00047 / 0.02 ( 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 171 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7613 (mpp) cc_final: 0.7316 (mpp) REVERT: A 205 MET cc_start: 0.7273 (ttm) cc_final: 0.6986 (ttp) REVERT: A 314 PHE cc_start: 0.8596 (t80) cc_final: 0.8319 (t80) REVERT: A 528 MET cc_start: 0.8071 (ppp) cc_final: 0.7659 (ppp) REVERT: A 550 LEU cc_start: 0.7927 (tp) cc_final: 0.7656 (tp) REVERT: A 595 ILE cc_start: 0.8414 (mp) cc_final: 0.8191 (mt) REVERT: A 619 ILE cc_start: 0.9083 (pt) cc_final: 0.8780 (mp) REVERT: A 627 GLN cc_start: 0.8324 (mm110) cc_final: 0.8057 (mp10) REVERT: C 777 ASP cc_start: 0.7638 (p0) cc_final: 0.7050 (p0) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1424 time to fit residues: 37.7436 Evaluate side-chains 120 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 74 optimal weight: 0.2980 chunk 147 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 202 optimal weight: 0.0980 chunk 207 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 191 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** 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 = 0.4090 r_free = 0.4090 target = 0.116008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092690 restraints weight = 56020.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090686 restraints weight = 83450.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.089558 restraints weight = 55958.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.089973 restraints weight = 52392.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089874 restraints weight = 36049.279| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19231 Z= 0.108 Angle : 0.684 10.435 26784 Z= 0.311 Chirality : 0.051 0.284 3154 Planarity : 0.004 0.043 2922 Dihedral : 13.326 163.231 3884 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.06 % Allowed : 1.02 % Favored : 98.92 % 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: -0.73 (0.19), residues: 1964 helix: 0.32 (0.18), residues: 894 sheet: -0.29 (0.36), residues: 214 loop : -1.37 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.016 0.001 TYR C 963 PHE 0.017 0.001 PHE C 710 TRP 0.019 0.001 TRP C 201 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (19228) covalent geometry : angle 0.68309 / 0.31 (26782) SS BOND : bond 0.00231 / 0.12 ( 1) SS BOND : angle 3.54467 / 1.97 ( 2) hydrogen bonds : bond 0.03041 / 1.99 ( 737) hydrogen bonds : angle 4.02943 / 2.79 ( 2024) Misc. bond : bond 0.00052 / 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 172 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7850 (mpp) cc_final: 0.7326 (mpp) REVERT: A 205 MET cc_start: 0.7290 (ttm) cc_final: 0.7028 (ttp) REVERT: A 314 PHE cc_start: 0.8534 (t80) cc_final: 0.8248 (t80) REVERT: A 528 MET cc_start: 0.8242 (ppp) cc_final: 0.7805 (ppp) REVERT: A 550 LEU cc_start: 0.7901 (tp) cc_final: 0.7629 (tp) REVERT: A 595 ILE cc_start: 0.8375 (mp) cc_final: 0.8159 (mt) REVERT: A 619 ILE cc_start: 0.9039 (pt) cc_final: 0.8724 (mp) REVERT: A 627 GLN cc_start: 0.8378 (mm110) cc_final: 0.8063 (mp10) REVERT: C 625 LEU cc_start: 0.8719 (tp) cc_final: 0.8514 (tp) REVERT: C 777 ASP cc_start: 0.7363 (p0) cc_final: 0.6971 (p0) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1313 time to fit residues: 36.0146 Evaluate side-chains 116 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 135 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 733 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.114047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090386 restraints weight = 57908.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088506 restraints weight = 83969.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.086528 restraints weight = 53001.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086918 restraints weight = 47732.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086922 restraints weight = 32800.275| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19231 Z= 0.136 Angle : 0.694 9.195 26784 Z= 0.322 Chirality : 0.051 0.275 3154 Planarity : 0.004 0.039 2922 Dihedral : 13.272 164.460 3884 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.06 % Allowed : 0.60 % Favored : 99.34 % 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: -0.76 (0.19), residues: 1964 helix: 0.26 (0.18), residues: 914 sheet: -0.25 (0.36), residues: 214 loop : -1.38 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 927 TYR 0.022 0.002 TYR A 230 PHE 0.026 0.001 PHE A 210 TRP 0.017 0.002 TRP C 201 HIS 0.008 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19228) covalent geometry : angle 0.69348 / 0.32 (26782) SS BOND : bond 0.00292 / 0.15 ( 1) SS BOND : angle 3.89061 / 2.20 ( 2) hydrogen bonds : bond 0.03422 / 2.25 ( 737) hydrogen bonds : angle 4.14975 / 2.88 ( 2024) Misc. bond : bond 0.00047 / 0.02 ( 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 156 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7978 (mpp) cc_final: 0.7633 (mpp) REVERT: A 528 MET cc_start: 0.8360 (ppp) cc_final: 0.7807 (ppp) REVERT: A 550 LEU cc_start: 0.7991 (tp) cc_final: 0.7697 (tp) REVERT: A 595 ILE cc_start: 0.8532 (mp) cc_final: 0.8283 (mm) REVERT: A 619 ILE cc_start: 0.9077 (pt) cc_final: 0.8801 (mp) REVERT: A 842 LEU cc_start: 0.8628 (pp) cc_final: 0.8324 (pp) REVERT: C 183 GLU cc_start: 0.7283 (tm-30) cc_final: 0.7005 (tm-30) REVERT: C 335 MET cc_start: 0.8601 (mmt) cc_final: 0.8285 (mmp) REVERT: C 625 LEU cc_start: 0.8807 (tp) cc_final: 0.8596 (tp) REVERT: C 777 ASP cc_start: 0.7477 (p0) cc_final: 0.7197 (p0) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1275 time to fit residues: 31.9556 Evaluate side-chains 112 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 200 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 60 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 167 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 733 HIS C 76 GLN C 185 ASN ** C 244 HIS ** 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 = 0.4071 r_free = 0.4071 target = 0.115012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090305 restraints weight = 57093.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.089768 restraints weight = 94729.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.088674 restraints weight = 50451.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089234 restraints weight = 38841.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.089180 restraints weight = 29695.292| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19231 Z= 0.110 Angle : 0.682 12.480 26784 Z= 0.311 Chirality : 0.051 0.268 3154 Planarity : 0.004 0.037 2922 Dihedral : 13.197 165.755 3884 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.06 % Allowed : 0.72 % Favored : 99.22 % 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: -0.71 (0.19), residues: 1964 helix: 0.32 (0.18), residues: 906 sheet: -0.20 (0.36), residues: 214 loop : -1.37 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.016 0.001 TYR A 230 PHE 0.017 0.001 PHE A 210 TRP 0.012 0.001 TRP C 201 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (19228) covalent geometry : angle 0.68180 / 0.31 (26782) SS BOND : bond 0.00167 / 0.09 ( 1) SS BOND : angle 3.52543 / 1.99 ( 2) hydrogen bonds : bond 0.03159 / 2.09 ( 737) hydrogen bonds : angle 4.03663 / 2.79 ( 2024) Misc. bond : bond 0.00054 / 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 157 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8047 (mpp) cc_final: 0.7710 (mpp) REVERT: A 528 MET cc_start: 0.8275 (ppp) cc_final: 0.7601 (ppp) REVERT: A 550 LEU cc_start: 0.7973 (tp) cc_final: 0.7683 (tp) REVERT: A 619 ILE cc_start: 0.9048 (pt) cc_final: 0.8743 (mp) REVERT: A 627 GLN cc_start: 0.8461 (mm110) cc_final: 0.7997 (mp10) REVERT: C 183 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 335 MET cc_start: 0.8438 (mmt) cc_final: 0.7878 (mpp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1255 time to fit residues: 32.1516 Evaluate side-chains 106 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 15 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 186 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 244 HIS A 341 GLN A 733 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.112843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.089658 restraints weight = 56630.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087250 restraints weight = 84268.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.086351 restraints weight = 54870.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.086720 restraints weight = 53324.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.086457 restraints weight = 39252.363| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19231 Z= 0.153 Angle : 0.717 9.196 26784 Z= 0.333 Chirality : 0.052 0.279 3154 Planarity : 0.004 0.036 2922 Dihedral : 13.221 167.205 3884 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.06 % Allowed : 0.36 % 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: -0.61 (0.19), residues: 1964 helix: 0.41 (0.18), residues: 896 sheet: -0.37 (0.35), residues: 214 loop : -1.25 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 112 TYR 0.028 0.002 TYR A 230 PHE 0.028 0.002 PHE A 210 TRP 0.031 0.002 TRP A 119 HIS 0.010 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (19228) covalent geometry : angle 0.71574 / 0.33 (26782) SS BOND : bond 0.00266 / 0.14 ( 1) SS BOND : angle 4.23944 / 2.43 ( 2) hydrogen bonds : bond 0.03654 / 2.40 ( 737) hydrogen bonds : angle 4.18718 / 2.89 ( 2024) Misc. bond : bond 0.00049 / 0.02 ( 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 147 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8040 (mpp) cc_final: 0.7622 (mpp) REVERT: A 280 ILE cc_start: 0.7841 (mm) cc_final: 0.7461 (mm) REVERT: A 528 MET cc_start: 0.8281 (ppp) cc_final: 0.7654 (ppp) REVERT: A 619 ILE cc_start: 0.9072 (pt) cc_final: 0.8756 (mp) REVERT: A 627 GLN cc_start: 0.8548 (mm110) cc_final: 0.8054 (mp10) REVERT: A 775 MET cc_start: 0.8408 (tmm) cc_final: 0.7593 (tmm) REVERT: A 839 LEU cc_start: 0.8925 (mm) cc_final: 0.8592 (tp) REVERT: C 661 LYS cc_start: 0.8462 (mtmm) cc_final: 0.7776 (tppt) REVERT: C 839 LEU cc_start: 0.9238 (tp) cc_final: 0.8949 (tp) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1345 time to fit residues: 31.6073 Evaluate side-chains 110 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 176 optimal weight: 0.0050 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS A 341 GLN A 733 HIS C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN C 570 ASN C 697 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.113913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.089867 restraints weight = 58982.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088777 restraints weight = 90796.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088277 restraints weight = 52523.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.088341 restraints weight = 55945.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.088521 restraints weight = 37515.998| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19231 Z= 0.117 Angle : 0.694 9.993 26784 Z= 0.317 Chirality : 0.051 0.299 3154 Planarity : 0.004 0.043 2922 Dihedral : 13.186 168.399 3884 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % 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: -0.58 (0.19), residues: 1964 helix: 0.46 (0.18), residues: 898 sheet: -0.46 (0.35), residues: 216 loop : -1.23 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 112 TYR 0.019 0.002 TYR A 230 PHE 0.016 0.001 PHE A 210 TRP 0.016 0.001 TRP A 119 HIS 0.005 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (19228) covalent geometry : angle 0.69306 / 0.32 (26782) SS BOND : bond 0.00206 / 0.11 ( 1) SS BOND : angle 3.58191 / 2.03 ( 2) hydrogen bonds : bond 0.03262 / 2.15 ( 737) hydrogen bonds : angle 4.02067 / 2.78 ( 2024) Misc. bond : bond 0.00053 / 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 143 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7989 (mpp) cc_final: 0.7444 (mpp) REVERT: A 280 ILE cc_start: 0.7774 (mm) cc_final: 0.7357 (mm) REVERT: A 528 MET cc_start: 0.8226 (ppp) cc_final: 0.7660 (ppp) REVERT: A 619 ILE cc_start: 0.9054 (pt) cc_final: 0.8740 (mp) REVERT: A 775 MET cc_start: 0.8428 (tmm) cc_final: 0.7682 (tmm) REVERT: A 839 LEU cc_start: 0.9003 (mm) cc_final: 0.8668 (tp) REVERT: C 125 GLU cc_start: 0.7346 (tp30) cc_final: 0.7023 (tp30) REVERT: C 661 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7922 (mmtt) REVERT: C 947 MET cc_start: 0.7807 (tmm) cc_final: 0.7477 (tmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1283 time to fit residues: 29.6630 Evaluate side-chains 105 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 153 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 38 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 106 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 341 GLN A 733 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.113961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093160 restraints weight = 58214.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.090516 restraints weight = 83624.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089095 restraints weight = 63147.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.089374 restraints weight = 64659.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.089304 restraints weight = 44401.177| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19231 Z= 0.111 Angle : 0.686 9.919 26784 Z= 0.311 Chirality : 0.051 0.311 3154 Planarity : 0.004 0.035 2922 Dihedral : 13.129 169.790 3884 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.53 (0.19), residues: 1964 helix: 0.46 (0.18), residues: 902 sheet: -0.41 (0.35), residues: 216 loop : -1.16 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 910 TYR 0.017 0.002 TYR A 230 PHE 0.016 0.001 PHE A 210 TRP 0.010 0.001 TRP A 198 HIS 0.007 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (19228) covalent geometry : angle 0.68537 / 0.31 (26782) SS BOND : bond 0.00167 / 0.09 ( 1) SS BOND : angle 3.52582 / 1.99 ( 2) hydrogen bonds : bond 0.03153 / 2.07 ( 737) hydrogen bonds : angle 3.93583 / 2.72 ( 2024) Misc. bond : bond 0.00057 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.39 seconds wall clock time: 53 minutes 12.45 seconds (3192.45 seconds total)