Starting phenix.real_space_refine on Thu Mar 5 01:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7abh_11696/03_2026/7abh_11696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7abh_11696/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7abh_11696/03_2026/7abh_11696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7abh_11696/03_2026/7abh_11696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7abh_11696/03_2026/7abh_11696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7abh_11696/03_2026/7abh_11696.map" } 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-dev-5986/lib/python3.9/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: {'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: {'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: {'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: {'GLU:plan': 7, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 4.80, per 1000 atoms: 0.27 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: 1.51 Conformation dependent library (CDL) restraints added in 1.2 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: 2.40 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: 3.82 Time building geometry restraints manager: 2.07 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: 24887 1.47 - 2.93: 596 2.93 - 4.40: 148 4.40 - 5.86: 56 5.86 - 7.33: 6 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: 10748 35.72 - 71.44: 145 71.44 - 107.16: 18 107.16 - 142.88: 1 142.88 - 178.60: 2 Dihedral angle restraints: 10914 sinusoidal: 1490 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 10911 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 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: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.530 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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= 0.218 Angle : 0.627 7.330 25693 Z= 0.362 Chirality : 0.046 0.209 3406 Planarity : 0.004 0.050 3492 Dihedral : 12.546 178.599 4752 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 covalent geometry : bond 0.00344 (18214) covalent geometry : angle 0.62678 (25693) hydrogen bonds : bond 0.13631 ( 1147) hydrogen bonds : angle 5.99072 ( 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 : 0.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0744 time to fit residues: 11.4618 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 : 0.536 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062477 restraints weight = 127523.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063034 restraints weight = 100278.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063153 restraints weight = 88530.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063565 restraints weight = 75622.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063690 restraints weight = 65617.334| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 18214 Z= 0.098 Angle : 0.482 7.750 25693 Z= 0.249 Chirality : 0.042 0.200 3406 Planarity : 0.004 0.048 3492 Dihedral : 12.766 171.412 4254 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % 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: -1.33 (0.15), residues: 3236 helix: 1.19 (0.15), residues: 1206 sheet: -2.21 (0.19), residues: 538 loop : -2.17 (0.16), residues: 1492 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 covalent geometry : bond 0.00192 (18214) covalent geometry : angle 0.48237 (25693) hydrogen bonds : bond 0.02686 ( 1147) hydrogen bonds : angle 4.11519 ( 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 : 0.573 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0715 time to fit residues: 11.2048 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 : 0.395 ------------------------------------------------------------------------------- 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: 0.6980 chunk 79 optimal weight: 4.9990 chunk 204 optimal weight: 30.0000 chunk 316 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 2 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.073810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059770 restraints weight = 128568.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.060157 restraints weight = 104952.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060252 restraints weight = 88550.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060427 restraints weight = 76147.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060491 restraints weight = 73987.686| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1883 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= 0.146 Angle : 0.534 9.374 25693 Z= 0.284 Chirality : 0.043 0.195 3406 Planarity : 0.004 0.046 3492 Dihedral : 12.991 169.663 4254 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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: -0.75 (0.16), residues: 3236 helix: 1.65 (0.16), residues: 1207 sheet: -1.89 (0.20), residues: 503 loop : -1.83 (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 covalent geometry : bond 0.00254 (18214) covalent geometry : angle 0.53424 (25693) hydrogen bonds : bond 0.03418 ( 1147) hydrogen bonds : angle 4.33266 ( 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 : 0.614 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0708 time to fit residues: 11.3606 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 : 0.588 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.068422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056500 restraints weight = 130584.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055471 restraints weight = 132947.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055440 restraints weight = 130124.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.055499 restraints weight = 108220.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055562 restraints weight = 97562.875| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 18214 Z= 0.420 Angle : 0.878 13.204 25693 Z= 0.509 Chirality : 0.050 0.246 3406 Planarity : 0.007 0.067 3492 Dihedral : 14.626 166.132 4254 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.71 % Favored : 88.16 % 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 : 0.61 % Twisted General : 0.06 % 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: -2.42 (0.14), residues: 3236 helix: -0.29 (0.14), residues: 1189 sheet: -2.10 (0.22), residues: 484 loop : -2.52 (0.16), residues: 1563 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 covalent geometry : bond 0.00678 (18214) covalent geometry : angle 0.87801 (25693) hydrogen bonds : bond 0.06038 ( 1147) hydrogen bonds : angle 6.85321 ( 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 77 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.616 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0742 time to fit residues: 11.5188 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 : 0.607 ------------------------------------------------------------------------------- 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: 1.9990 chunk 174 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 229 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.070453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057204 restraints weight = 128700.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057266 restraints weight = 116317.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057319 restraints weight = 99911.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057673 restraints weight = 89779.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057638 restraints weight = 83418.076| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3738 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= 0.175 Angle : 0.585 8.972 25693 Z= 0.318 Chirality : 0.044 0.182 3406 Planarity : 0.005 0.059 3492 Dihedral : 13.997 162.985 4254 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.46 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 : 0.03 % 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: -1.40 (0.15), residues: 3236 helix: 0.89 (0.15), residues: 1201 sheet: -1.72 (0.23), residues: 471 loop : -2.19 (0.16), residues: 1564 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 covalent geometry : bond 0.00290 (18214) covalent geometry : angle 0.58479 (25693) hydrogen bonds : bond 0.03556 ( 1147) hydrogen bonds : angle 5.17283 ( 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 : 0.575 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0744 time to fit residues: 11.8602 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 : 0.554 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 173 optimal weight: 0.0670 chunk 249 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 overall best weight: 1.9922 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.070874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057744 restraints weight = 127652.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057586 restraints weight = 126706.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057848 restraints weight = 104715.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057890 restraints weight = 93155.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057994 restraints weight = 87220.260| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3884 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= 0.147 Angle : 0.538 7.968 25693 Z= 0.286 Chirality : 0.043 0.133 3406 Planarity : 0.004 0.053 3492 Dihedral : 13.435 160.270 4254 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % 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: -0.80 (0.16), residues: 3236 helix: 1.65 (0.16), residues: 1205 sheet: -1.73 (0.22), residues: 513 loop : -1.96 (0.17), residues: 1518 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 covalent geometry : bond 0.00253 (18214) covalent geometry : angle 0.53760 (25693) hydrogen bonds : bond 0.03088 ( 1147) hydrogen bonds : angle 4.64605 ( 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 : 0.620 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0824 time to fit residues: 12.7901 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 : 0.643 ------------------------------------------------------------------------------- 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: 8.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.069325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056619 restraints weight = 129054.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056510 restraints weight = 120614.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056582 restraints weight = 105479.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056574 restraints weight = 97970.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056625 restraints weight = 94829.988| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18214 Z= 0.222 Angle : 0.623 8.597 25693 Z= 0.345 Chirality : 0.045 0.141 3406 Planarity : 0.005 0.053 3492 Dihedral : 13.776 159.272 4254 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % 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 : 0.03 % 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: -1.31 (0.15), residues: 3236 helix: 0.99 (0.15), residues: 1214 sheet: -1.73 (0.22), residues: 486 loop : -2.17 (0.16), residues: 1536 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 covalent geometry : bond 0.00361 (18214) covalent geometry : angle 0.62281 (25693) hydrogen bonds : bond 0.04060 ( 1147) hydrogen bonds : angle 5.46506 ( 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 : 0.601 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0730 time to fit residues: 11.6828 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 : 0.635 ------------------------------------------------------------------------------- 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: 0.0980 chunk 140 optimal weight: 0.0370 chunk 117 optimal weight: 1.9990 chunk 263 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058720 restraints weight = 127361.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058973 restraints weight = 123061.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059079 restraints weight = 99193.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059088 restraints weight = 87153.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059113 restraints weight = 94823.905| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18214 Z= 0.092 Angle : 0.490 7.696 25693 Z= 0.254 Chirality : 0.042 0.132 3406 Planarity : 0.004 0.054 3492 Dihedral : 13.192 158.131 4254 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -0.30 (0.16), residues: 3236 helix: 2.14 (0.16), residues: 1209 sheet: -1.40 (0.22), residues: 508 loop : -1.79 (0.17), residues: 1519 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 covalent geometry : bond 0.00183 (18214) covalent geometry : angle 0.49018 (25693) hydrogen bonds : bond 0.02480 ( 1147) hydrogen bonds : angle 4.19451 ( 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 : 0.648 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0754 time to fit residues: 12.0557 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 : 0.526 ------------------------------------------------------------------------------- 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: 7.9990 chunk 152 optimal weight: 0.5980 chunk 300 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 273 optimal weight: 0.1980 chunk 149 optimal weight: 5.9990 chunk 128 optimal weight: 0.0060 chunk 290 optimal weight: 10.0000 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.071848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058563 restraints weight = 127645.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058719 restraints weight = 112676.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058724 restraints weight = 96842.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058790 restraints weight = 89758.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058815 restraints weight = 87678.238| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18214 Z= 0.099 Angle : 0.481 7.611 25693 Z= 0.249 Chirality : 0.042 0.131 3406 Planarity : 0.004 0.055 3492 Dihedral : 12.997 158.133 4254 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % 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: -0.07 (0.16), residues: 3236 helix: 2.38 (0.16), residues: 1209 sheet: -1.33 (0.22), residues: 517 loop : -1.69 (0.17), residues: 1510 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 covalent geometry : bond 0.00192 (18214) covalent geometry : angle 0.48125 (25693) hydrogen bonds : bond 0.02433 ( 1147) hydrogen bonds : angle 4.04619 ( 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 : 0.471 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0745 time to fit residues: 11.7070 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 : 0.561 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 9.9990 chunk 219 optimal weight: 0.0010 chunk 277 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 322 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.9792 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.069018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056417 restraints weight = 128034.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056087 restraints weight = 112620.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056110 restraints weight = 108918.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.056126 restraints weight = 101160.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.056173 restraints weight = 97526.683| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18214 Z= 0.264 Angle : 0.645 8.138 25693 Z= 0.363 Chirality : 0.045 0.140 3406 Planarity : 0.005 0.055 3492 Dihedral : 13.635 158.216 4254 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % 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 : 0.03 % 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: -0.94 (0.16), residues: 3236 helix: 1.38 (0.15), residues: 1202 sheet: -1.55 (0.22), residues: 493 loop : -2.00 (0.17), residues: 1541 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 covalent geometry : bond 0.00427 (18214) covalent geometry : angle 0.64505 (25693) hydrogen bonds : bond 0.04139 ( 1147) hydrogen bonds : angle 5.39381 ( 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 78 residues out of total 2867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.603 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0752 time to fit residues: 11.7962 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 : 0.448 ------------------------------------------------------------------------------- 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: 6.9990 chunk 186 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 307 optimal weight: 20.0000 chunk 189 optimal weight: 0.0370 chunk 248 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.071674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.058590 restraints weight = 127435.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.058684 restraints weight = 107296.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058796 restraints weight = 97409.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058844 restraints weight = 80517.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058876 restraints weight = 83985.857| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4600 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= 0.092 Angle : 0.487 7.781 25693 Z= 0.253 Chirality : 0.042 0.136 3406 Planarity : 0.004 0.058 3492 Dihedral : 13.176 157.159 4254 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -0.16 (0.16), residues: 3236 helix: 2.28 (0.16), residues: 1208 sheet: -1.33 (0.22), residues: 512 loop : -1.72 (0.17), residues: 1516 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 covalent geometry : bond 0.00180 (18214) covalent geometry : angle 0.48719 (25693) hydrogen bonds : bond 0.02444 ( 1147) hydrogen bonds : angle 4.17007 ( 3229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.33 seconds wall clock time: 40 minutes 4.50 seconds (2404.50 seconds total)