Starting phenix.real_space_refine on Thu Mar 5 03:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk1_33240/03_2026/7xk1_33240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk1_33240/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk1_33240/03_2026/7xk1_33240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk1_33240/03_2026/7xk1_33240.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk1_33240/03_2026/7xk1_33240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk1_33240/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 7.09, per 1000 atoms: 0.38 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: 1.55 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: 2.34 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: 3.85 Time building geometry restraints manager: 2.11 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: 26257 1.83 - 3.66: 425 3.66 - 5.49: 70 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 - 30.00: 11161 30.00 - 59.99: 494 59.99 - 89.99: 132 89.99 - 119.98: 4 119.98 - 149.98: 2 Dihedral angle restraints: 11793 sinusoidal: 6077 harmonic: 5716 Sorted by residual: dihedral pdb=" O4' U D 19 " pdb=" C1' U D 19 " pdb=" N1 U D 19 " pdb=" C2 U D 19 " ideal model delta sinusoidal sigma weight residual 200.00 50.02 149.98 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 200.00 50.07 149.93 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 6.22 98.37 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 11790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2847 0.068 - 0.136: 283 0.136 - 0.205: 18 0.205 - 0.273: 4 0.273 - 0.341: 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 2.41 -2.75 -0.34 2.00e-01 2.50e+01 2.91e+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 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE A 969 " pdb=" CA ILE A 969 " pdb=" CG1 ILE A 969 " pdb=" CG2 ILE A 969 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+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: 0.03 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: 0.010 Normalize map: mean=0, sd=1: 3.730 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.830 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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= 0.333 Angle : 0.794 58.787 26784 Z= 0.415 Chirality : 0.042 0.341 3154 Planarity : 0.004 0.043 2922 Dihedral : 16.551 149.977 8094 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 covalent geometry : bond 0.00389 (19228) covalent geometry : angle 0.61080 (26782) SS BOND : bond 0.50506 ( 1) SS BOND : angle 58.70788 ( 2) hydrogen bonds : bond 0.16747 ( 737) hydrogen bonds : angle 7.19287 ( 2024) Misc. bond : bond 0.17610 ( 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 : 0.597 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: 0.1570 time to fit residues: 100.6086 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 : 0.567 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4140 r_free = 0.4140 target = 0.119500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.093081 restraints weight = 58858.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.094900 restraints weight = 102650.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096438 restraints weight = 53606.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.096775 restraints weight = 34649.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097376 restraints weight = 30249.963| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2975 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= 0.145 Angle : 0.661 11.493 26784 Z= 0.334 Chirality : 0.043 0.254 3154 Planarity : 0.005 0.050 2922 Dihedral : 17.644 150.746 4396 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % 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: -1.22 (0.19), residues: 1964 helix: -0.12 (0.18), residues: 894 sheet: -0.29 (0.35), residues: 226 loop : -1.66 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 735 TYR 0.021 0.002 TYR C 360 PHE 0.035 0.002 PHE C 710 TRP 0.013 0.001 TRP C 198 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00318 (19228) covalent geometry : angle 0.66013 (26782) SS BOND : bond 0.01015 ( 1) SS BOND : angle 3.94486 ( 2) hydrogen bonds : bond 0.04195 ( 737) hydrogen bonds : angle 4.41211 ( 2024) Misc. bond : bond 0.00045 ( 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 : 0.622 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: 0.8338 (tp) cc_final: 0.7984 (tp) REVERT: A 205 MET cc_start: 0.7007 (ttm) cc_final: 0.6805 (ttp) REVERT: A 314 PHE cc_start: 0.8034 (t80) cc_final: 0.7770 (t80) REVERT: A 352 ASN cc_start: 0.6951 (p0) cc_final: 0.6739 (p0) REVERT: A 389 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 573 LEU cc_start: 0.8309 (tp) cc_final: 0.8044 (tt) REVERT: A 619 ILE cc_start: 0.9059 (pt) cc_final: 0.8725 (mp) REVERT: A 842 LEU cc_start: 0.8562 (pp) cc_final: 0.8336 (pp) REVERT: A 869 VAL cc_start: 0.9109 (m) cc_final: 0.8696 (p) REVERT: C 205 MET cc_start: 0.6997 (mmm) cc_final: 0.6732 (mmm) REVERT: C 280 ILE cc_start: 0.7262 (mm) cc_final: 0.7022 (mm) REVERT: C 305 ASP cc_start: 0.6735 (t70) cc_final: 0.6475 (t70) REVERT: C 341 GLN cc_start: 0.7404 (pt0) cc_final: 0.7086 (tt0) REVERT: C 655 LEU cc_start: 0.8593 (mt) cc_final: 0.8239 (tt) REVERT: C 683 VAL cc_start: 0.8966 (t) cc_final: 0.8742 (m) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1317 time to fit residues: 48.6772 Evaluate side-chains 155 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 5.9990 chunk 139 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 660 GLN C 697 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.116183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.093700 restraints weight = 57698.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.092196 restraints weight = 84076.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.091475 restraints weight = 51918.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.091614 restraints weight = 54724.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091463 restraints weight = 42932.703| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19231 Z= 0.146 Angle : 0.614 9.101 26784 Z= 0.311 Chirality : 0.041 0.201 3154 Planarity : 0.005 0.060 2922 Dihedral : 17.510 152.422 4396 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.18 % Allowed : 1.81 % Favored : 98.01 % 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: -0.21 (0.18), residues: 890 sheet: -0.35 (0.34), residues: 226 loop : -1.54 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 419 TYR 0.024 0.002 TYR A 230 PHE 0.032 0.002 PHE C 710 TRP 0.023 0.002 TRP C 198 HIS 0.007 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00326 (19228) covalent geometry : angle 0.61370 (26782) SS BOND : bond 0.00500 ( 1) SS BOND : angle 3.60572 ( 2) hydrogen bonds : bond 0.03895 ( 737) hydrogen bonds : angle 4.37428 ( 2024) Misc. bond : bond 0.00049 ( 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 205 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.602 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: 0.7843 (mpp) cc_final: 0.7461 (mpt) REVERT: A 205 MET cc_start: 0.7255 (ttm) cc_final: 0.6995 (ttp) REVERT: A 314 PHE cc_start: 0.8311 (t80) cc_final: 0.8076 (t80) REVERT: A 619 ILE cc_start: 0.9069 (pt) cc_final: 0.8780 (mp) REVERT: A 842 LEU cc_start: 0.8598 (pp) cc_final: 0.8367 (pp) REVERT: A 869 VAL cc_start: 0.9149 (m) cc_final: 0.8690 (p) REVERT: C 205 MET cc_start: 0.7099 (mmm) cc_final: 0.6756 (mmm) REVERT: C 263 ASN cc_start: 0.7335 (t0) cc_final: 0.7113 (t0) REVERT: C 280 ILE cc_start: 0.7107 (mm) cc_final: 0.6844 (mm) REVERT: C 305 ASP cc_start: 0.6763 (t70) cc_final: 0.6489 (t70) REVERT: C 655 LEU cc_start: 0.8893 (mt) cc_final: 0.8354 (tt) REVERT: C 705 TYR cc_start: 0.9037 (m-10) cc_final: 0.8328 (m-10) REVERT: C 743 MET cc_start: 0.8802 (mmm) cc_final: 0.8451 (mmp) outliers start: 3 outliers final: 1 residues processed: 205 average time/residue: 0.1276 time to fit residues: 41.1664 Evaluate side-chains 134 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 0.7980 chunk 148 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 697 ASN A 733 HIS C 185 ASN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.114062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.090487 restraints weight = 56450.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.088495 restraints weight = 87733.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.087814 restraints weight = 54060.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087872 restraints weight = 55877.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087683 restraints weight = 41636.466| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 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 = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19231 Z= 0.151 Angle : 0.629 10.866 26784 Z= 0.316 Chirality : 0.041 0.176 3154 Planarity : 0.005 0.061 2922 Dihedral : 17.521 153.718 4396 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % 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: -1.09 (0.19), residues: 1964 helix: -0.03 (0.18), residues: 890 sheet: -0.70 (0.35), residues: 226 loop : -1.40 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 910 TYR 0.026 0.002 TYR C 250 PHE 0.030 0.002 PHE A 210 TRP 0.015 0.002 TRP A 119 HIS 0.007 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00343 (19228) covalent geometry : angle 0.62853 (26782) SS BOND : bond 0.00707 ( 1) SS BOND : angle 3.49653 ( 2) hydrogen bonds : bond 0.03650 ( 737) hydrogen bonds : angle 4.36472 ( 2024) Misc. bond : bond 0.00040 ( 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 181 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.626 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: 0.7837 (mpp) cc_final: 0.7604 (mpp) REVERT: A 205 MET cc_start: 0.7327 (ttm) cc_final: 0.7020 (ttp) REVERT: A 314 PHE cc_start: 0.8574 (t80) cc_final: 0.8309 (t80) REVERT: A 528 MET cc_start: 0.8318 (ppp) cc_final: 0.7848 (ppp) REVERT: A 550 LEU cc_start: 0.7922 (tp) cc_final: 0.7643 (tp) REVERT: A 619 ILE cc_start: 0.9108 (pt) cc_final: 0.8798 (mp) REVERT: A 869 VAL cc_start: 0.9157 (m) cc_final: 0.8807 (p) REVERT: C 705 TYR cc_start: 0.8790 (m-10) cc_final: 0.8580 (m-10) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.1381 time to fit residues: 38.9579 Evaluate side-chains 114 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 138 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 478 ASN A 733 HIS ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.114556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088923 restraints weight = 56643.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.089127 restraints weight = 93930.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.087822 restraints weight = 48701.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.088193 restraints weight = 43514.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088278 restraints weight = 30991.719| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 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 = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4930 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= 0.118 Angle : 0.592 12.117 26784 Z= 0.294 Chirality : 0.040 0.180 3154 Planarity : 0.004 0.050 2922 Dihedral : 17.480 154.351 4396 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.06 % Allowed : 1.33 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1964 helix: 0.17 (0.18), residues: 898 sheet: -0.37 (0.35), residues: 214 loop : -1.40 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 910 TYR 0.021 0.002 TYR A 230 PHE 0.018 0.001 PHE A 210 TRP 0.020 0.001 TRP C 201 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00267 (19228) covalent geometry : angle 0.59132 (26782) SS BOND : bond 0.00306 ( 1) SS BOND : angle 3.89653 ( 2) hydrogen bonds : bond 0.03342 ( 737) hydrogen bonds : angle 4.21331 ( 2024) Misc. bond : bond 0.00043 ( 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 172 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.511 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: A 93 MET cc_start: 0.7967 (mpp) cc_final: 0.7577 (mpp) REVERT: A 528 MET cc_start: 0.8292 (ppp) cc_final: 0.7867 (ppp) REVERT: A 550 LEU cc_start: 0.7921 (tp) cc_final: 0.7634 (tp) REVERT: A 595 ILE cc_start: 0.8419 (mp) cc_final: 0.8192 (mt) REVERT: A 619 ILE cc_start: 0.9094 (pt) cc_final: 0.8784 (mp) REVERT: A 627 GLN cc_start: 0.8363 (mm110) cc_final: 0.8109 (mp10) REVERT: A 869 VAL cc_start: 0.9108 (m) cc_final: 0.8759 (p) REVERT: C 625 LEU cc_start: 0.8754 (tp) cc_final: 0.8541 (tp) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1271 time to fit residues: 34.4473 Evaluate side-chains 118 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 0.0060 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.0010 chunk 191 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 660 GLN A 697 ASN A 733 HIS C 185 ASN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.114522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.090945 restraints weight = 56181.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.089288 restraints weight = 83561.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087388 restraints weight = 50283.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087780 restraints weight = 44141.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.088428 restraints weight = 30793.532| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 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 = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5192 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= 0.112 Angle : 0.580 8.435 26784 Z= 0.288 Chirality : 0.040 0.178 3154 Planarity : 0.004 0.069 2922 Dihedral : 17.423 154.882 4396 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.12 % Allowed : 1.20 % Favored : 98.67 % 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: 0.31 (0.18), residues: 894 sheet: -0.36 (0.35), residues: 214 loop : -1.33 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 499 TYR 0.018 0.002 TYR A 230 PHE 0.017 0.001 PHE A 210 TRP 0.015 0.001 TRP C 201 HIS 0.005 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00246 (19228) covalent geometry : angle 0.57939 (26782) SS BOND : bond 0.00293 ( 1) SS BOND : angle 3.67000 ( 2) hydrogen bonds : bond 0.03223 ( 737) hydrogen bonds : angle 4.10924 ( 2024) Misc. bond : bond 0.00044 ( 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 165 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8019 (mpp) cc_final: 0.7419 (mpp) REVERT: A 528 MET cc_start: 0.8395 (ppp) cc_final: 0.7906 (ppp) REVERT: A 550 LEU cc_start: 0.8049 (tp) cc_final: 0.7758 (tp) REVERT: A 595 ILE cc_start: 0.8487 (mp) cc_final: 0.8281 (mt) REVERT: A 619 ILE cc_start: 0.9089 (pt) cc_final: 0.8772 (mp) REVERT: A 869 VAL cc_start: 0.9139 (m) cc_final: 0.8826 (p) REVERT: C 335 MET cc_start: 0.8551 (mmt) cc_final: 0.8122 (mmp) REVERT: C 625 LEU cc_start: 0.8796 (tp) cc_final: 0.8591 (tp) outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 0.1344 time to fit residues: 34.8659 Evaluate side-chains 119 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 0.7980 chunk 177 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 162 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 33 optimal weight: 0.0060 chunk 135 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 733 HIS C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.114625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.090831 restraints weight = 57134.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.089008 restraints weight = 86886.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087967 restraints weight = 52622.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.088307 restraints weight = 54205.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088195 restraints weight = 37916.324| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 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 = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5350 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= 0.108 Angle : 0.584 9.130 26784 Z= 0.290 Chirality : 0.040 0.178 3154 Planarity : 0.005 0.138 2922 Dihedral : 17.407 155.174 4396 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: -0.71 (0.19), residues: 1964 helix: 0.37 (0.18), residues: 892 sheet: -0.23 (0.37), residues: 200 loop : -1.38 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.019 0.001 TYR A 230 PHE 0.016 0.001 PHE A 210 TRP 0.011 0.001 TRP C 201 HIS 0.007 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00240 (19228) covalent geometry : angle 0.58279 (26782) SS BOND : bond 0.00243 ( 1) SS BOND : angle 3.59152 ( 2) hydrogen bonds : bond 0.03222 ( 737) hydrogen bonds : angle 4.07992 ( 2024) Misc. bond : bond 0.00045 ( 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 162 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.664 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: A 93 MET cc_start: 0.7988 (mpp) cc_final: 0.7613 (mpp) REVERT: A 528 MET cc_start: 0.8396 (ppp) cc_final: 0.7756 (ppp) REVERT: A 619 ILE cc_start: 0.9047 (pt) cc_final: 0.8734 (mp) REVERT: A 627 GLN cc_start: 0.8432 (mm110) cc_final: 0.8082 (mp10) REVERT: A 869 VAL cc_start: 0.9136 (m) cc_final: 0.8794 (p) REVERT: A 871 ILE cc_start: 0.9127 (tp) cc_final: 0.8913 (tp) REVERT: C 125 GLU cc_start: 0.7016 (tp30) cc_final: 0.6789 (tp30) REVERT: C 335 MET cc_start: 0.8500 (mmt) cc_final: 0.7869 (mpp) REVERT: C 625 LEU cc_start: 0.8798 (tp) cc_final: 0.8578 (tp) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1305 time to fit residues: 33.7814 Evaluate side-chains 113 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 105 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 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 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.114246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090894 restraints weight = 57119.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088907 restraints weight = 81450.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087760 restraints weight = 51579.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088096 restraints weight = 54479.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087983 restraints weight = 37451.720| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 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 = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19231 Z= 0.110 Angle : 0.586 9.604 26784 Z= 0.289 Chirality : 0.040 0.177 3154 Planarity : 0.005 0.136 2922 Dihedral : 17.374 155.418 4396 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % 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: -0.72 (0.19), residues: 1964 helix: 0.34 (0.18), residues: 906 sheet: -0.38 (0.35), residues: 214 loop : -1.36 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 724 TYR 0.019 0.002 TYR A 230 PHE 0.016 0.001 PHE A 210 TRP 0.010 0.001 TRP C 530 HIS 0.006 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00245 (19228) covalent geometry : angle 0.58475 (26782) SS BOND : bond 0.00247 ( 1) SS BOND : angle 3.61961 ( 2) hydrogen bonds : bond 0.03166 ( 737) hydrogen bonds : angle 4.03927 ( 2024) Misc. bond : bond 0.00046 ( 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 155 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8028 (mpp) cc_final: 0.7597 (mpp) REVERT: A 528 MET cc_start: 0.8412 (ppp) cc_final: 0.7739 (ppp) REVERT: A 619 ILE cc_start: 0.9061 (pt) cc_final: 0.8732 (mp) REVERT: A 627 GLN cc_start: 0.8525 (mm110) cc_final: 0.8107 (mp10) REVERT: A 839 LEU cc_start: 0.9020 (mm) cc_final: 0.8820 (mm) REVERT: A 869 VAL cc_start: 0.9161 (m) cc_final: 0.8860 (p) REVERT: C 335 MET cc_start: 0.8527 (mmt) cc_final: 0.7906 (mpp) REVERT: C 659 MET cc_start: 0.8610 (mtm) cc_final: 0.8179 (mtm) REVERT: C 661 LYS cc_start: 0.8598 (mttp) cc_final: 0.8086 (tppt) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1289 time to fit residues: 32.2471 Evaluate side-chains 108 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 0.8980 chunk 135 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 697 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.113433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086595 restraints weight = 56422.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087666 restraints weight = 98444.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087414 restraints weight = 43944.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087844 restraints weight = 37493.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087754 restraints weight = 29595.873| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 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 = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5828 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= 0.120 Angle : 0.597 12.847 26784 Z= 0.293 Chirality : 0.040 0.175 3154 Planarity : 0.004 0.035 2922 Dihedral : 17.381 155.387 4396 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: -0.65 (0.19), residues: 1964 helix: 0.37 (0.18), residues: 902 sheet: -0.43 (0.35), residues: 216 loop : -1.26 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.022 0.002 TYR A 230 PHE 0.022 0.001 PHE A 210 TRP 0.009 0.001 TRP C 530 HIS 0.007 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00272 (19228) covalent geometry : angle 0.59578 (26782) SS BOND : bond 0.00228 ( 1) SS BOND : angle 3.87948 ( 2) hydrogen bonds : bond 0.03338 ( 737) hydrogen bonds : angle 4.05016 ( 2024) Misc. bond : bond 0.00046 ( 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 154 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.579 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: 0.7995 (mpp) cc_final: 0.7504 (mpp) REVERT: A 528 MET cc_start: 0.8375 (ppp) cc_final: 0.7675 (ppp) REVERT: A 619 ILE cc_start: 0.9071 (pt) cc_final: 0.8734 (mp) REVERT: A 627 GLN cc_start: 0.8478 (mm110) cc_final: 0.8015 (mp10) REVERT: A 839 LEU cc_start: 0.8921 (mm) cc_final: 0.8613 (tp) REVERT: A 842 LEU cc_start: 0.8569 (pp) cc_final: 0.8329 (pp) REVERT: C 625 LEU cc_start: 0.8813 (tp) cc_final: 0.8598 (tp) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1310 time to fit residues: 31.9797 Evaluate side-chains 111 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 0.0040 chunk 103 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 0.0000 chunk 176 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.113060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090534 restraints weight = 58609.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088319 restraints weight = 82917.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.086789 restraints weight = 55591.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.086952 restraints weight = 60359.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.086722 restraints weight = 43446.782| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19231 Z= 0.122 Angle : 0.598 9.546 26784 Z= 0.295 Chirality : 0.040 0.172 3154 Planarity : 0.004 0.036 2922 Dihedral : 17.384 155.293 4396 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.62 (0.19), residues: 1964 helix: 0.41 (0.18), residues: 906 sheet: -0.48 (0.35), residues: 216 loop : -1.25 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 724 TYR 0.022 0.002 TYR A 230 PHE 0.026 0.001 PHE C 710 TRP 0.011 0.001 TRP C 530 HIS 0.006 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00276 (19228) covalent geometry : angle 0.59713 (26782) SS BOND : bond 0.00185 ( 1) SS BOND : angle 3.74770 ( 2) hydrogen bonds : bond 0.03301 ( 737) hydrogen bonds : angle 4.03851 ( 2024) Misc. bond : bond 0.00046 ( 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 150 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8025 (mpp) cc_final: 0.7455 (mpp) REVERT: A 206 GLU cc_start: 0.7281 (tt0) cc_final: 0.6955 (tt0) REVERT: A 280 ILE cc_start: 0.7847 (mm) cc_final: 0.7430 (mm) REVERT: A 528 MET cc_start: 0.8252 (ppp) cc_final: 0.7765 (ppp) REVERT: A 619 ILE cc_start: 0.9049 (pt) cc_final: 0.8718 (mp) REVERT: A 839 LEU cc_start: 0.8947 (mm) cc_final: 0.8615 (tp) REVERT: A 842 LEU cc_start: 0.8669 (pp) cc_final: 0.8432 (pp) REVERT: C 625 LEU cc_start: 0.8819 (tp) cc_final: 0.8609 (tp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1293 time to fit residues: 31.0596 Evaluate side-chains 104 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 726 GLN A 733 HIS ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.111635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.088995 restraints weight = 57675.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086191 restraints weight = 88500.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085507 restraints weight = 55826.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085376 restraints weight = 56459.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.085285 restraints weight = 42700.278| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19231 Z= 0.156 Angle : 0.629 10.400 26784 Z= 0.313 Chirality : 0.041 0.171 3154 Planarity : 0.004 0.051 2922 Dihedral : 17.444 154.861 4396 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.06 % Allowed : 0.12 % Favored : 99.82 % 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: -0.64 (0.19), residues: 1964 helix: 0.40 (0.18), residues: 906 sheet: -0.53 (0.35), residues: 216 loop : -1.25 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 144 TYR 0.027 0.002 TYR A 230 PHE 0.039 0.002 PHE C 710 TRP 0.009 0.002 TRP A 201 HIS 0.010 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00356 (19228) covalent geometry : angle 0.62822 (26782) SS BOND : bond 0.00340 ( 1) SS BOND : angle 4.07932 ( 2) hydrogen bonds : bond 0.03644 ( 737) hydrogen bonds : angle 4.15391 ( 2024) Misc. bond : bond 0.00042 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2975.60 seconds wall clock time: 52 minutes 22.41 seconds (3142.41 seconds total)