Starting phenix.real_space_refine (version: dev) on Wed Feb 22 16:37:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abh_11696/02_2023/7abh_11696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abh_11696/02_2023/7abh_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abh_11696/02_2023/7abh_11696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abh_11696/02_2023/7abh_11696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abh_11696/02_2023/7abh_11696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abh_11696/02_2023/7abh_11696.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 156 Chain: "Z" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 579 Classifications: {'RNA': 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: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} 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: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 6} 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: {'GLN:plan1': 34, 'HIS:plan': 21, 'TYR:plan': 39, 'ASN:plan1': 33, 'TRP:plan': 7, 'ASP:plan': 49, 'PHE:plan': 23, 'GLU:plan': 64, 'ARG:plan': 57} 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: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 8, 'GLU:plan': 14, 'ARG:plan': 11} 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: {'GLN:plan1': 47, 'ASP:plan': 63, 'TYR:plan': 37, 'ASN:plan1': 55, 'TRP:plan': 7, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 86, 'ARG:plan': 60} 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: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS: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: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} 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: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 15} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "2" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 778 Classifications: {'RNA': 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: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 11.63, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 8.38 Conformation dependent library (CDL) restraints added in 3.9 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: 5.36 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: 8.77 Time building geometry restraints manager: 8.99 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: 100.81 - 107.23: 1056 107.23 - 113.65: 10187 113.65 - 120.07: 4888 120.07 - 126.49: 9251 126.49 - 132.91: 311 Bond angle restraints: 25693 Sorted by residual: 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 angle pdb=" CA LYS u1102 " pdb=" C LYS u1102 " pdb=" O LYS u1102 " ideal model delta sigma weight residual 122.45 118.02 4.43 1.30e+00 5.92e-01 1.16e+01 ... (remaining 25688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 10630 35.72 - 71.44: 56 71.44 - 107.16: 7 107.16 - 142.88: 1 142.88 - 178.60: 2 Dihedral angle restraints: 10696 sinusoidal: 1272 harmonic: 9424 Sorted by residual: dihedral pdb=" O4' C Z 162 " pdb=" C1' C Z 162 " pdb=" N1 C Z 162 " pdb=" C2 C Z 162 " ideal model delta sinusoidal sigma weight residual 200.00 35.26 164.74 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' C 2 45 " pdb=" C1' C 2 45 " pdb=" N1 C 2 45 " pdb=" C2 C 2 45 " ideal model delta sinusoidal sigma weight residual -160.00 -93.87 -66.13 1 1.50e+01 4.44e-03 2.54e+01 dihedral pdb=" C4' U 2 46 " pdb=" C3' U 2 46 " pdb=" O3' U 2 46 " pdb=" P U 2 47 " ideal model delta sinusoidal sigma weight residual 250.00 71.40 178.60 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 10693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2539 0.042 - 0.084: 540 0.084 - 0.126: 286 0.126 - 0.167: 30 0.167 - 0.209: 11 Chirality restraints: 3406 Sorted by residual: chirality pdb=" CA VAL u1110 " pdb=" N VAL u1110 " pdb=" C VAL u1110 " pdb=" CB VAL u1110 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL E 920 " pdb=" N VAL E 920 " pdb=" C VAL E 920 " pdb=" CB VAL E 920 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE E 407 " pdb=" N ILE E 407 " pdb=" C ILE E 407 " pdb=" CB ILE E 407 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+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 2.440 nonbonded pdb=" N2 G Z 146 " pdb=" O4 U 2 41 " model vdw 2.209 2.520 nonbonded pdb=" O2 U 2 54 " pdb=" N6 A 2 59 " model vdw 2.225 2.520 ... (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 ========== 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 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. 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.830 Check model and map are aligned: 0.260 Process input model: 58.560 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.010 ------------------------------------------------------------------------------- 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 : 0.003 0.036 18214 Z= 0.250 Angle : 0.627 7.330 25693 Z= 0.362 Chirality : 0.046 0.209 3406 Planarity : 0.004 0.050 3492 Dihedral : 9.267 178.599 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.177 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1683 time to fit residues: 27.5225 Evaluate side-chains 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 296 optimal weight: 20.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 18214 Z= 0.293 Angle : 0.671 12.836 25693 Z= 0.378 Chirality : 0.046 0.215 3406 Planarity : 0.005 0.057 3492 Dihedral : 10.315 173.946 4036 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.71 % Favored : 91.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 3236 helix: 0.53 (0.15), residues: 1210 sheet: -2.31 (0.19), residues: 534 loop : -2.27 (0.17), residues: 1492 *********************** 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 fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.886 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1685 time to fit residues: 27.6650 Evaluate side-chains 76 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 247 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 297 optimal weight: 30.0000 chunk 321 optimal weight: 6.9990 chunk 264 optimal weight: 30.0000 chunk 295 optimal weight: 0.0010 chunk 101 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 overall best weight: 5.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 18214 Z= 0.388 Angle : 0.797 13.623 25693 Z= 0.456 Chirality : 0.048 0.203 3406 Planarity : 0.006 0.067 3492 Dihedral : 11.718 165.955 4036 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.48 % Favored : 87.39 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.14), residues: 3236 helix: -0.30 (0.14), residues: 1197 sheet: -2.23 (0.21), residues: 477 loop : -2.70 (0.15), residues: 1562 *********************** 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 80 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 2.038 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.1759 time to fit residues: 29.2342 Evaluate side-chains 78 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1477 time to fit residues: 2.8601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 141 optimal weight: 0.0060 chunk 199 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 316 optimal weight: 7.9990 chunk 155 optimal weight: 0.0870 chunk 282 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 2.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18214 Z= 0.220 Angle : 0.599 9.868 25693 Z= 0.327 Chirality : 0.044 0.189 3406 Planarity : 0.005 0.060 3492 Dihedral : 10.768 162.605 4036 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.67 % Favored : 90.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 3236 helix: 0.74 (0.15), residues: 1205 sheet: -2.00 (0.22), residues: 501 loop : -2.33 (0.16), residues: 1530 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1720 time to fit residues: 28.6774 Evaluate side-chains 79 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 30.0000 chunk 179 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 269 optimal weight: 0.0980 chunk 218 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 0.0030 chunk 283 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18214 Z= 0.246 Angle : 0.615 9.695 25693 Z= 0.338 Chirality : 0.045 0.142 3406 Planarity : 0.005 0.049 3492 Dihedral : 10.670 159.790 4036 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.08 % Favored : 87.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3236 helix: 0.90 (0.15), residues: 1208 sheet: -1.83 (0.22), residues: 477 loop : -2.31 (0.16), residues: 1551 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1702 time to fit residues: 27.9575 Evaluate side-chains 79 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 316 optimal weight: 0.0470 chunk 262 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 0.0070 chunk 166 optimal weight: 5.9990 overall best weight: 2.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4379 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= 0.191 Angle : 0.551 7.742 25693 Z= 0.296 Chirality : 0.044 0.137 3406 Planarity : 0.004 0.052 3492 Dihedral : 10.245 158.470 4036 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.84 % Favored : 91.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 3236 helix: 1.40 (0.16), residues: 1206 sheet: -1.83 (0.22), residues: 511 loop : -2.10 (0.17), residues: 1519 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.864 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1677 time to fit residues: 27.5034 Evaluate side-chains 79 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 315 optimal weight: 0.0770 chunk 197 optimal weight: 0.0050 chunk 192 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 overall best weight: 4.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 18214 Z= 0.335 Angle : 0.694 10.548 25693 Z= 0.393 Chirality : 0.046 0.158 3406 Planarity : 0.006 0.070 3492 Dihedral : 11.033 157.844 4036 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.81 % Favored : 86.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 3236 helix: 0.46 (0.15), residues: 1201 sheet: -1.92 (0.22), residues: 467 loop : -2.43 (0.16), residues: 1568 *********************** 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 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1764 time to fit residues: 28.1455 Evaluate side-chains 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 188 optimal weight: 40.0000 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 247 optimal weight: 0.0980 chunk 286 optimal weight: 6.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 18214 Z= 0.250 Angle : 0.614 9.286 25693 Z= 0.339 Chirality : 0.045 0.152 3406 Planarity : 0.005 0.058 3492 Dihedral : 10.753 157.195 4036 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.43 % Favored : 88.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3236 helix: 0.78 (0.15), residues: 1205 sheet: -2.00 (0.22), residues: 493 loop : -2.35 (0.16), residues: 1538 *********************** 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 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1767 time to fit residues: 28.8289 Evaluate side-chains 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 chunk 265 optimal weight: 30.0000 chunk 277 optimal weight: 7.9990 chunk 292 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18214 Z= 0.250 Angle : 0.606 8.779 25693 Z= 0.334 Chirality : 0.045 0.143 3406 Planarity : 0.005 0.056 3492 Dihedral : 10.702 156.122 4036 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.95 % Favored : 87.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3236 helix: 0.92 (0.15), residues: 1209 sheet: -1.90 (0.22), residues: 488 loop : -2.38 (0.16), residues: 1539 *********************** 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 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1703 time to fit residues: 28.2281 Evaluate side-chains 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 0.8980 chunk 189 optimal weight: 0.2980 chunk 147 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 325 optimal weight: 20.0000 chunk 299 optimal weight: 0.0770 chunk 259 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 18214 Z= 0.164 Angle : 0.529 7.698 25693 Z= 0.282 Chirality : 0.043 0.138 3406 Planarity : 0.005 0.050 3492 Dihedral : 10.268 155.855 4036 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 3236 helix: 1.57 (0.16), residues: 1212 sheet: -1.76 (0.22), residues: 506 loop : -2.15 (0.17), residues: 1518 ********************** 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 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.891 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1732 time to fit residues: 27.9994 Evaluate side-chains 77 residues out of total 2867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 108 optimal weight: 0.0170 chunk 266 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 228 optimal weight: 0.8980 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057024 restraints weight = 127414.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057610 restraints weight = 104894.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057756 restraints weight = 88008.596| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5086 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= 0.144 Angle : 0.496 7.621 25693 Z= 0.259 Chirality : 0.042 0.133 3406 Planarity : 0.004 0.050 3492 Dihedral : 9.883 155.854 4036 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 3236 helix: 2.05 (0.16), residues: 1212 sheet: -1.59 (0.23), residues: 507 loop : -1.90 (0.17), residues: 1517 =============================================================================== Job complete usr+sys time: 2411.28 seconds wall clock time: 43 minutes 52.60 seconds (2632.60 seconds total)