Starting phenix.real_space_refine on Sat Sep 12 20:18:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.map" model { file = "/net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7abh_11696/09_2026/7abh_11696.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians P 65 5.49 5 C 10598 2.51 5 N 3501 2.21 5 O 3758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17922 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 237 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TRP:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "y" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 498 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'ARG:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 156 Chain: "Z" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 579 Classifications: {'RNAv2': 28} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 16} Link IDs: {'rna2p': 4, 'rna3p': 23} Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 6, 'ARG:plan': 7, 'ASP:plan': 3, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 1, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 149 Chain: "4" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 541 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 4, 'TRANS': 103} Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TYR:plan': 7, 'TRP:plan': 4, 'HIS:plan': 5, 'ASN:plan1': 8, 'GLU:plan': 9, 'ARG:plan': 6, 'PHE:plan': 3, 'GLN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 250 Chain: "u" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 4704 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 754} Link IDs: {'PTRANS': 49, 'TRANS': 882} Chain breaks: 4 Unresolved non-hydrogen bonds: 2792 Unresolved non-hydrogen angles: 3558 Unresolved non-hydrogen dihedrals: 2280 Unresolved non-hydrogen chiralities: 289 Planarities with less than four sites: {'GLU:plan': 64, 'TYR:plan': 39, 'HIS:plan': 21, 'ARG:plan': 57, 'ASP:plan': 49, 'ASN:plan1': 33, 'PHE:plan': 23, 'GLN:plan1': 34, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 1502 Chain: "T" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 942 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 19, 'TRANS': 163} Chain breaks: 3 Unresolved non-hydrogen bonds: 588 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 11, 'PHE:plan': 8, 'GLU:plan': 14, 'GLN:plan1': 8, 'ASP:plan': 11, 'HIS:plan': 5, 'TRP:plan': 3, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 337 Chain: "E" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 5926 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 960} Link IDs: {'PTRANS': 60, 'TRANS': 1116} Chain breaks: 5 Unresolved non-hydrogen bonds: 3435 Unresolved non-hydrogen angles: 4412 Unresolved non-hydrogen dihedrals: 2784 Unresolved non-hydrogen chiralities: 354 Planarities with less than four sites: {'PHE:plan': 57, 'TYR:plan': 37, 'ASN:plan1': 55, 'GLN:plan1': 47, 'ARG:plan': 60, 'HIS:plan': 26, 'GLU:plan': 86, 'ASP:plan': 63, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 1980 Chain: "w" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 391 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 4, 'GLU:plan': 6, 'TRP:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "x" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 397 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 4, 'TYR:plan': 5, 'HIS:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 176 Chain: "z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 544 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 8, 'ASN:plan1': 8, 'TYR:plan': 10, 'ASP:plan': 5, 'PHE:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 222 Chain: "0" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 761 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 10, 'TRANS': 139} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 5, 'ARG:plan': 15, 'TYR:plan': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 312 Chain: "1" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 607 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 10, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'TYR:plan': 5, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 223 Chain: "Y" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 478 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 4, 'TRANS': 90} Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 6, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 153 Chain: "2" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 778 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna2p': 5, 'rna3p': 31} Chain: "7" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 165 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 4.45, per 1000 atoms: 0.25 Number of scatterers: 17922 At special positions: 0 Unit cell: (172.84, 154.28, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 65 15.00 O 3758 8.00 N 3501 7.00 C 10598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 34 sheets defined 41.3% alpha, 15.4% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'L' and resid 12 through 26 Processing helix chain 'L' and resid 30 through 36 removed outlier: 3.670A pdb=" N ILE L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 53 Processing helix chain 'y' and resid 51 through 55 removed outlier: 3.760A pdb=" N TYR y 54 " --> pdb=" O TYR y 51 " (cutoff:3.500A) Processing helix chain 'y' and resid 73 through 78 Processing helix chain 'F' and resid 20 through 42 Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 78 through 90 removed outlier: 3.634A pdb=" N ARG F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG F 85 " --> pdb=" O ASN F 81 " (cutoff:3.500A) Processing helix chain '4' and resid 393 through 400 Processing helix chain '4' and resid 418 through 427 Processing helix chain '4' and resid 428 through 439 Processing helix chain '4' and resid 451 through 462 removed outlier: 3.665A pdb=" N ALA 4 455 " --> pdb=" O GLN 4 451 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL 4 456 " --> pdb=" O ILE 4 452 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER 4 457 " --> pdb=" O GLU 4 453 " (cutoff:3.500A) Processing helix chain '4' and resid 488 through 498 Processing helix chain 'u' and resid 119 through 126 removed outlier: 3.552A pdb=" N HIS u 122 " --> pdb=" O TYR u 119 " (cutoff:3.500A) Processing helix chain 'u' and resid 312 through 326 Processing helix chain 'u' and resid 326 through 335 Processing helix chain 'u' and resid 400 through 408 removed outlier: 3.629A pdb=" N PHE u 408 " --> pdb=" O LEU u 404 " (cutoff:3.500A) Processing helix chain 'u' and resid 421 through 426 Processing helix chain 'u' and resid 427 through 432 Processing helix chain 'u' and resid 468 through 473 removed outlier: 3.983A pdb=" N GLN u 473 " --> pdb=" O PRO u 469 " (cutoff:3.500A) Processing helix chain 'u' and resid 475 through 480 removed outlier: 3.522A pdb=" N LEU u 479 " --> pdb=" O PHE u 475 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL u 480 " --> pdb=" O ASP u 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 475 through 480' Processing helix chain 'u' and resid 491 through 498 Processing helix chain 'u' and resid 499 through 506 removed outlier: 3.985A pdb=" N LYS u 503 " --> pdb=" O LYS u 499 " (cutoff:3.500A) Processing helix chain 'u' and resid 508 through 522 Processing helix chain 'u' and resid 522 through 527 Processing helix chain 'u' and resid 527 through 540 Proline residue: u 537 - end of helix Processing helix chain 'u' and resid 545 through 563 removed outlier: 3.706A pdb=" N LYS u 562 " --> pdb=" O ARG u 558 " (cutoff:3.500A) Processing helix chain 'u' and resid 570 through 583 removed outlier: 3.886A pdb=" N VAL u 577 " --> pdb=" O LYS u 573 " (cutoff:3.500A) Proline residue: u 580 - end of helix Processing helix chain 'u' and resid 586 through 604 Processing helix chain 'u' and resid 605 through 614 Processing helix chain 'u' and resid 621 through 640 Processing helix chain 'u' and resid 640 through 653 removed outlier: 3.597A pdb=" N LEU u 644 " --> pdb=" O GLY u 640 " (cutoff:3.500A) Proline residue: u 646 - end of helix Processing helix chain 'u' and resid 657 through 676 removed outlier: 3.624A pdb=" N ARG u 661 " --> pdb=" O SER u 657 " (cutoff:3.500A) Processing helix chain 'u' and resid 677 through 681 Proline residue: u 681 - end of helix Processing helix chain 'u' and resid 682 through 691 Processing helix chain 'u' and resid 692 through 694 No H-bonds generated for 'chain 'u' and resid 692 through 694' Processing helix chain 'u' and resid 698 through 716 Processing helix chain 'u' and resid 724 through 726 No H-bonds generated for 'chain 'u' and resid 724 through 726' Processing helix chain 'u' and resid 727 through 737 removed outlier: 3.755A pdb=" N LEU u 731 " --> pdb=" O VAL u 727 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP u 732 " --> pdb=" O LEU u 728 " (cutoff:3.500A) Processing helix chain 'u' and resid 740 through 754 removed outlier: 3.652A pdb=" N ALA u 744 " --> pdb=" O GLY u 740 " (cutoff:3.500A) Processing helix chain 'u' and resid 758 through 776 removed outlier: 4.069A pdb=" N TYR u 764 " --> pdb=" O GLU u 760 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU u 771 " --> pdb=" O ARG u 767 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE u 772 " --> pdb=" O GLU u 768 " (cutoff:3.500A) Processing helix chain 'u' and resid 777 through 779 No H-bonds generated for 'chain 'u' and resid 777 through 779' Processing helix chain 'u' and resid 781 through 797 removed outlier: 3.813A pdb=" N GLY u 797 " --> pdb=" O LYS u 793 " (cutoff:3.500A) Processing helix chain 'u' and resid 802 through 810 Processing helix chain 'u' and resid 810 through 817 Processing helix chain 'u' and resid 822 through 825 Processing helix chain 'u' and resid 826 through 845 removed outlier: 3.544A pdb=" N ARG u 831 " --> pdb=" O ARG u 827 " (cutoff:3.500A) Processing helix chain 'u' and resid 845 through 855 removed outlier: 4.166A pdb=" N ILE u 849 " --> pdb=" O GLY u 845 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP u 855 " --> pdb=" O SER u 851 " (cutoff:3.500A) Processing helix chain 'u' and resid 856 through 859 Processing helix chain 'u' and resid 861 through 879 Processing helix chain 'u' and resid 880 through 884 removed outlier: 4.019A pdb=" N ASP u 883 " --> pdb=" O GLY u 880 " (cutoff:3.500A) Processing helix chain 'u' and resid 885 through 902 Processing helix chain 'u' and resid 907 through 922 removed outlier: 4.622A pdb=" N LEU u 911 " --> pdb=" O ASP u 907 " (cutoff:3.500A) Processing helix chain 'u' and resid 923 through 926 Processing helix chain 'u' and resid 927 through 942 removed outlier: 4.629A pdb=" N GLN u 931 " --> pdb=" O PRO u 927 " (cutoff:3.500A) Processing helix chain 'u' and resid 947 through 965 removed outlier: 5.110A pdb=" N VAL u 960 " --> pdb=" O SER u 956 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL u 961 " --> pdb=" O ARG u 957 " (cutoff:3.500A) Processing helix chain 'u' and resid 967 through 982 Processing helix chain 'u' and resid 986 through 1004 Processing helix chain 'u' and resid 1012 through 1021 Proline residue: u1018 - end of helix Processing helix chain 'u' and resid 1022 through 1027 removed outlier: 3.500A pdb=" N LYS u1025 " --> pdb=" O PRO u1022 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG u1027 " --> pdb=" O LEU u1024 " (cutoff:3.500A) Processing helix chain 'u' and resid 1028 through 1046 Processing helix chain 'u' and resid 1051 through 1063 Processing helix chain 'u' and resid 1064 through 1068 removed outlier: 3.582A pdb=" N LYS u1067 " --> pdb=" O GLU u1064 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA u1068 " --> pdb=" O LEU u1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 1064 through 1068' Processing helix chain 'u' and resid 1071 through 1088 Processing helix chain 'u' and resid 1089 through 1099 removed outlier: 3.955A pdb=" N VAL u1093 " --> pdb=" O GLY u1089 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN u1099 " --> pdb=" O ALA u1095 " (cutoff:3.500A) Processing helix chain 'u' and resid 1110 through 1123 Processing helix chain 'u' and resid 1124 through 1136 Proline residue: u1130 - end of helix Processing helix chain 'u' and resid 1140 through 1159 Processing helix chain 'u' and resid 1160 through 1164 removed outlier: 4.013A pdb=" N ASP u1164 " --> pdb=" O MET u1161 " (cutoff:3.500A) Processing helix chain 'u' and resid 1165 through 1177 Proline residue: u1171 - end of helix Processing helix chain 'u' and resid 1181 through 1199 Processing helix chain 'u' and resid 1204 through 1216 removed outlier: 3.857A pdb=" N TYR u1214 " --> pdb=" O HIS u1210 " (cutoff:3.500A) Processing helix chain 'u' and resid 1217 through 1220 Processing helix chain 'u' and resid 1223 through 1241 Processing helix chain 'u' and resid 1242 through 1251 Processing helix chain 'u' and resid 1259 through 1275 removed outlier: 4.042A pdb=" N GLY u1275 " --> pdb=" O SER u1271 " (cutoff:3.500A) Processing helix chain 'u' and resid 1279 through 1284 removed outlier: 3.861A pdb=" N HIS u1283 " --> pdb=" O ALA u1279 " (cutoff:3.500A) Processing helix chain 'u' and resid 1297 through 1302 Processing helix chain 'T' and resid 461 through 469 Processing helix chain 'T' and resid 471 through 475 Processing helix chain 'T' and resid 476 through 480 removed outlier: 3.506A pdb=" N ASP T 479 " --> pdb=" O GLU T 476 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL T 480 " --> pdb=" O MET T 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 476 through 480' Processing helix chain 'T' and resid 484 through 493 Processing helix chain 'T' and resid 501 through 505 removed outlier: 3.710A pdb=" N TRP T 504 " --> pdb=" O PRO T 501 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS T 505 " --> pdb=" O ARG T 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 501 through 505' Processing helix chain 'T' and resid 525 through 530 Processing helix chain 'T' and resid 532 through 545 Processing helix chain 'T' and resid 568 through 577 Processing helix chain 'T' and resid 610 through 618 removed outlier: 3.960A pdb=" N ARG T 614 " --> pdb=" O SER T 610 " (cutoff:3.500A) Processing helix chain 'T' and resid 631 through 640 removed outlier: 4.204A pdb=" N ALA T 635 " --> pdb=" O PRO T 631 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET T 636 " --> pdb=" O TRP T 632 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN T 637 " --> pdb=" O LEU T 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.581A pdb=" N ASP E 195 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 Processing helix chain 'E' and resid 808 through 825 Processing helix chain 'E' and resid 838 through 845 Processing helix chain 'E' and resid 1134 through 1152 removed outlier: 4.096A pdb=" N SER E1150 " --> pdb=" O MET E1146 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1165 Processing helix chain 'E' and resid 1175 through 1180 Processing helix chain 'E' and resid 1180 through 1185 removed outlier: 4.061A pdb=" N SER E1184 " --> pdb=" O GLU E1180 " (cutoff:3.500A) Processing helix chain 'E' and resid 1186 through 1198 Processing helix chain 'E' and resid 1200 through 1216 removed outlier: 3.627A pdb=" N ILE E1211 " --> pdb=" O LYS E1207 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 37 removed outlier: 3.858A pdb=" N ALA w 36 " --> pdb=" O LEU w 32 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 73 removed outlier: 3.505A pdb=" N ALA w 67 " --> pdb=" O SER w 63 " (cutoff:3.500A) Processing helix chain 'x' and resid 27 through 46 Processing helix chain 'x' and resid 46 through 55 Processing helix chain 'x' and resid 60 through 71 Processing helix chain 'z' and resid 31 through 40 Processing helix chain 'z' and resid 66 through 77 removed outlier: 3.513A pdb=" N ALA z 70 " --> pdb=" O ASP z 66 " (cutoff:3.500A) Processing helix chain 'z' and resid 105 through 117 removed outlier: 4.063A pdb=" N GLN z 109 " --> pdb=" O LYS z 105 " (cutoff:3.500A) Processing helix chain '0' and resid 230 through 237 Processing helix chain '1' and resid 4 through 20 removed outlier: 3.812A pdb=" N LYS 1 8 " --> pdb=" O LEU 1 4 " (cutoff:3.500A) Processing helix chain '1' and resid 23 through 27 removed outlier: 3.708A pdb=" N SER 1 27 " --> pdb=" O ASP 1 24 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 57 Processing helix chain '1' and resid 58 through 60 No H-bonds generated for 'chain '1' and resid 58 through 60' Processing helix chain '1' and resid 86 through 97 Processing helix chain 'Y' and resid 32 through 36 removed outlier: 3.990A pdb=" N LYS Y 36 " --> pdb=" O CYS Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 43 removed outlier: 3.763A pdb=" N VAL Y 43 " --> pdb=" O MET Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 60 Processing helix chain 'Y' and resid 64 through 75 removed outlier: 4.136A pdb=" N ILE Y 68 " --> pdb=" O ASP Y 64 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU Y 75 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 93 removed outlier: 3.614A pdb=" N MET Y 85 " --> pdb=" O ASP Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 115 Proline residue: Y 107 - end of helix Processing helix chain 'Y' and resid 121 through 126 removed outlier: 3.517A pdb=" N GLU Y 125 " --> pdb=" O SER Y 121 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Y 126 " --> pdb=" O ALA Y 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 121 through 126' Processing helix chain '7' and resid 148 through 179 Processing sheet with id=AA1, first strand: chain 'y' and resid 15 through 19 removed outlier: 4.601A pdb=" N ALA y 18 " --> pdb=" O ILE y 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'y' and resid 21 through 23 removed outlier: 3.637A pdb=" N SER y 67 " --> pdb=" O LEU y 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'y' and resid 39 through 42 removed outlier: 3.588A pdb=" N THR y 41 " --> pdb=" O TYR y 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 46 through 48 Processing sheet with id=AA5, first strand: chain '4' and resid 406 through 408 Processing sheet with id=AA6, first strand: chain 'u' and resid 413 through 414 Processing sheet with id=AA7, first strand: chain 'E' and resid 1117 through 1119 removed outlier: 6.625A pdb=" N ILE E1126 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 16 through 20 Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 68 removed outlier: 3.544A pdb=" N MET E 66 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE E 68 " --> pdb=" O TYR E 77 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 88 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER E 82 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE E 87 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN E 104 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE E 89 " --> pdb=" O ILE E 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AB2, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 165 through 172 removed outlier: 6.492A pdb=" N LEU E 185 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL E 170 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA E 183 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY E 172 " --> pdb=" O MET E 181 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET E 181 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU E 212 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG E 222 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP E 214 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL E 220 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 232 through 238 removed outlier: 6.831A pdb=" N CYS E 251 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU E 235 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU E 249 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR E 237 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY E 247 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 273 through 274 removed outlier: 6.380A pdb=" N ARG E 273 " --> pdb=" O PHE E 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 289 through 294 removed outlier: 3.644A pdb=" N CYS E 289 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 300 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE E 299 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU E 315 " --> pdb=" O PHE E 299 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE E 310 " --> pdb=" O PHE E 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 336 through 342 removed outlier: 3.618A pdb=" N PHE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU E 358 " --> pdb=" O VAL E 398 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 407 through 413 removed outlier: 3.682A pdb=" N PHE E 409 " --> pdb=" O ALA E 426 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 445 through 450 removed outlier: 6.750A pdb=" N ILE E 764 " --> pdb=" O MET E 447 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL E 449 " --> pdb=" O LEU E 762 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 762 " --> pdb=" O VAL E 449 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 761 " --> pdb=" O SER E 758 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 458 through 462 removed outlier: 4.111A pdb=" N VAL E 484 " --> pdb=" O VAL E 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 507 through 510 Processing sheet with id=AC3, first strand: chain 'E' and resid 544 through 549 Processing sheet with id=AC4, first strand: chain 'E' and resid 587 through 592 removed outlier: 3.739A pdb=" N CYS E 589 " --> pdb=" O GLY E 608 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR E 613 " --> pdb=" O LEU E 609 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL E 614 " --> pdb=" O MET E 630 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N MET E 630 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE E 616 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN E 626 " --> pdb=" O SER E 618 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 637 through 643 removed outlier: 3.752A pdb=" N LEU E 674 " --> pdb=" O THR E 689 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 689 " --> pdb=" O LEU E 674 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 700 through 706 Processing sheet with id=AC7, first strand: chain 'E' and resid 721 through 724 removed outlier: 3.771A pdb=" N THR E 732 " --> pdb=" O LEU E 721 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 785 through 790 removed outlier: 5.204A pdb=" N THR E 802 " --> pdb=" O PRO E 785 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 787 " --> pdb=" O ILE E 800 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 797 " --> pdb=" O MET E 869 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 886 through 895 removed outlier: 7.047A pdb=" N GLY E 908 " --> pdb=" O PHE E 889 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL E 891 " --> pdb=" O LEU E 906 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU E 906 " --> pdb=" O VAL E 891 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 893 " --> pdb=" O TYR E 904 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR E 904 " --> pdb=" O VAL E 893 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY E 922 " --> pdb=" O LYS E 911 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY E 923 " --> pdb=" O VAL E 945 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR E 943 " --> pdb=" O VAL E 925 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 949 through 955 removed outlier: 4.511A pdb=" N ALA E 951 " --> pdb=" O GLY E 962 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU E 967 " --> pdb=" O GLU E 982 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU E 982 " --> pdb=" O LEU E 967 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 969 " --> pdb=" O LYS E 980 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 990 through 995 Processing sheet with id=AD3, first strand: chain 'E' and resid 1036 through 1038 removed outlier: 7.324A pdb=" N ILE E1053 " --> pdb=" O ASN E1094 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN E1094 " --> pdb=" O ILE E1053 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL E1055 " --> pdb=" O ILE E1092 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E1057 " --> pdb=" O GLU E1090 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU E1090 " --> pdb=" O ARG E1057 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'w' and resid 41 through 43 Processing sheet with id=AD5, first strand: chain 'w' and resid 78 through 79 removed outlier: 3.577A pdb=" N LYS w 82 " --> pdb=" O LEU w 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '0' and resid 307 through 314 removed outlier: 4.018A pdb=" N GLN 0 307 " --> pdb=" O TYR 0 327 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1' and resid 62 through 67 1128 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 3368 1.30 - 1.37: 3573 1.37 - 1.45: 1009 1.45 - 1.53: 9563 1.53 - 1.61: 701 Bond restraints: 18214 Sorted by residual: bond pdb=" N GLY E1113 " pdb=" CA GLY E1113 " ideal model delta sigma weight residual 1.444 1.475 -0.031 9.30e-03 1.16e+04 1.13e+01 bond pdb=" C GLN 4 472 " pdb=" N PRO 4 473 " ideal model delta sigma weight residual 1.336 1.368 -0.032 9.80e-03 1.04e+04 1.06e+01 bond pdb=" N LEU E 913 " pdb=" CA LEU E 913 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.16e-02 7.43e+03 8.97e+00 bond pdb=" N ILE E 914 " pdb=" CA ILE E 914 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.22e-02 6.72e+03 8.93e+00 bond pdb=" N THR E 943 " pdb=" CA THR E 943 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.16e-02 7.43e+03 8.39e+00 ... (remaining 18209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 24685 1.47 - 2.93: 741 2.93 - 4.40: 194 4.40 - 5.86: 67 5.86 - 7.33: 6 Bond angle restraints: 25693 Sorted by residual: angle pdb=" C3' U 2 46 " pdb=" O3' U 2 46 " pdb=" P U 2 47 " ideal model delta sigma weight residual 119.70 124.52 -4.82 1.20e+00 6.94e-01 1.61e+01 angle pdb=" CA GLY E 923 " pdb=" C GLY E 923 " pdb=" O GLY E 923 " ideal model delta sigma weight residual 121.57 118.11 3.46 8.70e-01 1.32e+00 1.58e+01 angle pdb=" N LEU u1101 " pdb=" CA LEU u1101 " pdb=" C LEU u1101 " ideal model delta sigma weight residual 113.18 108.75 4.43 1.21e+00 6.83e-01 1.34e+01 angle pdb=" CA LYS E 942 " pdb=" C LYS E 942 " pdb=" O LYS E 942 " ideal model delta sigma weight residual 121.67 118.29 3.38 9.30e-01 1.16e+00 1.32e+01 angle pdb=" N LEU E 770 " pdb=" CA LEU E 770 " pdb=" C LEU E 770 " ideal model delta sigma weight residual 113.28 109.04 4.24 1.22e+00 6.72e-01 1.21e+01 ... (remaining 25688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 10564 35.72 - 71.44: 126 71.44 - 107.16: 5 107.16 - 142.88: 0 142.88 - 178.60: 1 Dihedral angle restraints: 10696 sinusoidal: 1272 harmonic: 9424 Sorted by residual: dihedral pdb=" C4' A 2 29 " pdb=" C3' A 2 29 " pdb=" C2' A 2 29 " pdb=" C1' A 2 29 " ideal model delta sinusoidal sigma weight residual 36.35 -36.82 73.17 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' U 2 47 " pdb=" C3' U 2 47 " pdb=" C2' U 2 47 " pdb=" C1' U 2 47 " ideal model delta sinusoidal sigma weight residual 36.34 -35.94 72.29 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U Z 166 " pdb=" C3' U Z 166 " pdb=" C2' U Z 166 " pdb=" C1' U Z 166 " ideal model delta sinusoidal sigma weight residual 36.34 -35.83 72.18 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 10693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2753 0.062 - 0.123: 522 0.123 - 0.185: 44 0.185 - 0.246: 57 0.246 - 0.308: 30 Chirality restraints: 3406 Sorted by residual: chirality pdb=" C2' U 2 46 " pdb=" C3' U 2 46 " pdb=" O2' U 2 46 " pdb=" C1' U 2 46 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" P U Z 153 " pdb=" OP1 U Z 153 " pdb=" OP2 U Z 153 " pdb=" O5' U Z 153 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" P A Z 149 " pdb=" OP1 A Z 149 " pdb=" OP2 A Z 149 " pdb=" O5' A Z 149 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3403 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 43 " -0.031 2.00e-02 2.50e+03 1.58e-02 5.63e+00 pdb=" N1 U 2 43 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U 2 43 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 2 43 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U 2 43 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U 2 43 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U 2 43 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U 2 43 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U 2 43 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO u1011 " 0.034 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO u1012 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO u1012 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO u1012 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 44 " -0.026 2.00e-02 2.50e+03 1.31e-02 3.86e+00 pdb=" N1 U 2 44 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U 2 44 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U 2 44 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U 2 44 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U 2 44 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U 2 44 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U 2 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 3 2.20 - 2.88: 6927 2.88 - 3.55: 25063 3.55 - 4.23: 32569 4.23 - 4.90: 53691 Nonbonded interactions: 118253 Sorted by model distance: nonbonded pdb=" CB LYS E1106 " pdb=" CA LEU E1117 " model vdw 1.529 3.870 nonbonded pdb=" O4 U Z 156 " pdb=" O6 G 2 33 " model vdw 2.156 2.432 nonbonded pdb=" O2' U 2 44 " pdb=" O5' C 2 45 " model vdw 2.162 3.040 nonbonded pdb=" N2 G Z 146 " pdb=" O4 U 2 41 " model vdw 2.209 3.120 nonbonded pdb=" O2 U 2 54 " pdb=" N6 A 2 59 " model vdw 2.225 3.120 ... (remaining 118248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.004 0.036 18214 Z= 0.220 Angle : 0.679 7.330 25693 Z= 0.370 Chirality : 0.060 0.308 3406 Planarity : 0.004 0.050 3492 Dihedral : 10.891 178.599 4534 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.03 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.14), residues: 3236 helix: -0.28 (0.14), residues: 1169 sheet: -2.89 (0.18), residues: 546 loop : -2.71 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.22 (18214) covalent geometry : angle 0.67893 / 0.37 (25693) hydrogen bonds : bond 0.13631 / 9.35 ( 1147) hydrogen bonds : angle 5.99072 / 3.97 ( 3229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0779 time to fit residues: 12.3170 Evaluate side-chains 77 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0050 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.0170 overall best weight: 0.6634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.076880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062537 restraints weight = 127531.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063165 restraints weight = 103219.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063296 restraints weight = 83733.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063508 restraints weight = 72647.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063536 restraints weight = 72427.109| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 18214 Z= 0.116 Angle : 0.677 24.755 25693 Z= 0.296 Chirality : 0.057 0.909 3406 Planarity : 0.004 0.047 3492 Dihedral : 10.319 170.319 4036 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.15), residues: 3236 helix: 1.07 (0.15), residues: 1206 sheet: -2.21 (0.19), residues: 525 loop : -2.26 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (18214) covalent geometry : angle 0.67676 / 0.30 (25693) hydrogen bonds : bond 0.02978 / 2.03 ( 1147) hydrogen bonds : angle 4.28753 / 2.86 ( 3229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.636 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0738 time to fit residues: 11.6812 Evaluate side-chains 77 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 111 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058701 restraints weight = 129632.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059122 restraints weight = 105728.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059242 restraints weight = 79870.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059294 restraints weight = 71898.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.059338 restraints weight = 73294.565| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18214 Z= 0.223 Angle : 0.725 10.452 25693 Z= 0.357 Chirality : 0.053 0.500 3406 Planarity : 0.004 0.050 3492 Dihedral : 10.795 178.675 4036 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.15), residues: 3236 helix: 1.25 (0.16), residues: 1202 sheet: -1.95 (0.20), residues: 529 loop : -2.01 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.22 (18214) covalent geometry : angle 0.72507 / 0.36 (25693) hydrogen bonds : bond 0.04134 / 2.76 ( 1147) hydrogen bonds : angle 5.00493 / 3.27 ( 3229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.677 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0784 time to fit residues: 12.6231 Evaluate side-chains 77 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 149 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 300 optimal weight: 0.0870 chunk 269 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.057467 restraints weight = 129286.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057961 restraints weight = 101429.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058335 restraints weight = 84554.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058662 restraints weight = 74613.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058777 restraints weight = 67603.761| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18214 Z= 0.190 Angle : 0.678 11.558 25693 Z= 0.330 Chirality : 0.051 0.416 3406 Planarity : 0.004 0.054 3492 Dihedral : 10.898 166.754 4036 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.16), residues: 3236 helix: 1.35 (0.16), residues: 1208 sheet: -1.82 (0.21), residues: 497 loop : -1.96 (0.17), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.19 (18214) covalent geometry : angle 0.67765 / 0.33 (25693) hydrogen bonds : bond 0.03551 / 2.39 ( 1147) hydrogen bonds : angle 4.84356 / 3.19 ( 3229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.645 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0769 time to fit residues: 12.3703 Evaluate side-chains 78 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 48 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 249 optimal weight: 0.0970 chunk 167 optimal weight: 0.0270 chunk 318 optimal weight: 0.9980 chunk 283 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 overall best weight: 0.9638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059843 restraints weight = 129317.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059914 restraints weight = 111935.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059897 restraints weight = 101661.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059936 restraints weight = 94554.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060017 restraints weight = 95091.519| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18214 Z= 0.107 Angle : 0.580 12.109 25693 Z= 0.269 Chirality : 0.049 0.428 3406 Planarity : 0.004 0.056 3492 Dihedral : 10.359 157.714 4036 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.16), residues: 3236 helix: 2.17 (0.16), residues: 1199 sheet: -1.58 (0.21), residues: 526 loop : -1.70 (0.17), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.11 (18214) covalent geometry : angle 0.57958 / 0.27 (25693) hydrogen bonds : bond 0.02617 / 1.76 ( 1147) hydrogen bonds : angle 4.03288 / 2.70 ( 3229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.713 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0736 time to fit residues: 11.7557 Evaluate side-chains 78 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 324 optimal weight: 8.9990 chunk 37 optimal weight: 0.0570 chunk 295 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 249 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 268 optimal weight: 7.9990 overall best weight: 2.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057712 restraints weight = 128665.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.057809 restraints weight = 110249.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057850 restraints weight = 99771.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057862 restraints weight = 89593.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057924 restraints weight = 88259.773| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18214 Z= 0.192 Angle : 0.671 11.908 25693 Z= 0.327 Chirality : 0.050 0.433 3406 Planarity : 0.004 0.046 3492 Dihedral : 10.736 158.173 4036 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.16), residues: 3236 helix: 1.77 (0.16), residues: 1203 sheet: -1.58 (0.22), residues: 507 loop : -1.76 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.19 (18214) covalent geometry : angle 0.67131 / 0.33 (25693) hydrogen bonds : bond 0.03635 / 2.43 ( 1147) hydrogen bonds : angle 4.76815 / 3.14 ( 3229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.672 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0767 time to fit residues: 12.3524 Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 261 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 163 optimal weight: 0.0870 chunk 157 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.071252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.057531 restraints weight = 128668.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057792 restraints weight = 113697.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057987 restraints weight = 93082.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057994 restraints weight = 78986.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058064 restraints weight = 82843.570| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18214 Z= 0.166 Angle : 0.635 11.644 25693 Z= 0.307 Chirality : 0.050 0.430 3406 Planarity : 0.004 0.051 3492 Dihedral : 10.666 157.676 4036 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.16), residues: 3236 helix: 1.88 (0.16), residues: 1207 sheet: -1.49 (0.22), residues: 517 loop : -1.76 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.17 (18214) covalent geometry : angle 0.63462 / 0.31 (25693) hydrogen bonds : bond 0.03191 / 2.13 ( 1147) hydrogen bonds : angle 4.55149 / 3.02 ( 3229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.621 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0768 time to fit residues: 12.3683 Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 108 optimal weight: 0.0270 chunk 140 optimal weight: 0.0970 chunk 117 optimal weight: 0.3980 chunk 263 optimal weight: 3.9990 chunk 43 optimal weight: 0.0170 chunk 66 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 overall best weight: 0.9076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059053 restraints weight = 128434.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059441 restraints weight = 114647.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059506 restraints weight = 89298.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059572 restraints weight = 87361.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059619 restraints weight = 84500.434| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18214 Z= 0.097 Angle : 0.566 11.634 25693 Z= 0.263 Chirality : 0.048 0.418 3406 Planarity : 0.004 0.047 3492 Dihedral : 10.237 158.457 4036 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.16), residues: 3236 helix: 2.47 (0.16), residues: 1207 sheet: -1.28 (0.22), residues: 520 loop : -1.52 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 (18214) covalent geometry : angle 0.56577 / 0.26 (25693) hydrogen bonds : bond 0.02523 / 1.69 ( 1147) hydrogen bonds : angle 3.90465 / 2.62 ( 3229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.683 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0762 time to fit residues: 12.2484 Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 321 optimal weight: 5.9990 chunk 152 optimal weight: 0.0980 chunk 300 optimal weight: 0.6980 chunk 309 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 290 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060464 restraints weight = 129266.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060612 restraints weight = 114966.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.060708 restraints weight = 93935.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.060769 restraints weight = 85767.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.060869 restraints weight = 82870.781| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18214 Z= 0.086 Angle : 0.540 11.678 25693 Z= 0.248 Chirality : 0.048 0.419 3406 Planarity : 0.004 0.052 3492 Dihedral : 9.945 160.496 4036 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.16), residues: 3236 helix: 2.68 (0.16), residues: 1219 sheet: -1.07 (0.22), residues: 519 loop : -1.38 (0.18), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (18214) covalent geometry : angle 0.53976 / 0.25 (25693) hydrogen bonds : bond 0.02201 / 1.47 ( 1147) hydrogen bonds : angle 3.51373 / 2.36 ( 3229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0781 time to fit residues: 12.5855 Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 219 optimal weight: 0.1980 chunk 277 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 139 optimal weight: 0.0470 chunk 318 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 322 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059430 restraints weight = 128016.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059219 restraints weight = 110282.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059209 restraints weight = 104094.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059206 restraints weight = 99997.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059322 restraints weight = 91066.237| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18214 Z= 0.129 Angle : 0.574 11.352 25693 Z= 0.271 Chirality : 0.048 0.416 3406 Planarity : 0.004 0.049 3492 Dihedral : 10.112 161.175 4036 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.16), residues: 3236 helix: 2.65 (0.16), residues: 1221 sheet: -1.13 (0.22), residues: 521 loop : -1.35 (0.18), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (18214) covalent geometry : angle 0.57419 / 0.27 (25693) hydrogen bonds : bond 0.02674 / 1.79 ( 1147) hydrogen bonds : angle 3.83954 / 2.56 ( 3229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.715 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0775 time to fit residues: 12.2487 Evaluate side-chains 79 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 230 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 307 optimal weight: 20.0000 chunk 189 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.072682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059161 restraints weight = 128704.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059353 restraints weight = 115674.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059431 restraints weight = 97515.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059457 restraints weight = 91246.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.059496 restraints weight = 86713.240| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18214 Z= 0.100 Angle : 0.553 11.239 25693 Z= 0.257 Chirality : 0.048 0.413 3406 Planarity : 0.004 0.052 3492 Dihedral : 10.061 160.602 4036 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.16), residues: 3236 helix: 2.74 (0.16), residues: 1215 sheet: -1.08 (0.23), residues: 516 loop : -1.30 (0.18), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR L 26 PHE 0.000 0.000 PHE y 10 TRP 0.000 0.000 TRP L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 (18214) covalent geometry : angle 0.55331 / 0.26 (25693) hydrogen bonds : bond 0.02455 / 1.64 ( 1147) hydrogen bonds : angle 3.69716 / 2.47 ( 3229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.72 seconds wall clock time: 43 minutes 26.27 seconds (2606.27 seconds total)