Starting phenix.real_space_refine on Sun Jul 5 11:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m98_63729/07_2026/9m98_63729_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m98_63729/07_2026/9m98_63729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m98_63729/07_2026/9m98_63729_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m98_63729/07_2026/9m98_63729_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m98_63729/07_2026/9m98_63729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m98_63729/07_2026/9m98_63729.map" } resolution = 3.47 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= 0.002 sd= 0.038 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 98 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 16552 2.51 5 N 4791 2.21 5 O 5344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26876 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1658 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1753 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8520 Classifications: {'peptide': 1123} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1060} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "D" Number of atoms: 9769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1260, 9769 Classifications: {'peptide': 1260} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1199} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "M" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1234 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 954 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 945 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DT:plan': 1, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12409 SG CYS D 60 36.400 50.791 119.722 1.00179.91 S ATOM 12427 SG CYS D 62 36.417 47.615 121.629 1.00171.93 S ATOM 12536 SG CYS D 75 35.508 51.099 123.256 1.00171.90 S ATOM 12562 SG CYS D 78 38.944 50.369 122.716 1.00176.46 S ATOM 18971 SG CYS D 891 46.983 110.244 87.133 1.00128.77 S ATOM 19533 SG CYS D 968 48.958 107.204 88.593 1.00130.06 S ATOM 19575 SG CYS D 975 47.341 107.035 85.211 1.00117.32 S ATOM 19593 SG CYS D 978 50.258 109.133 85.491 1.00119.30 S Time building chain proxies: 4.59, per 1000 atoms: 0.17 Number of scatterers: 26876 At special positions: 0 Unit cell: (138.84, 143.29, 195.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 88 16.00 P 98 15.00 Mg 1 11.99 O 5344 8.00 N 4791 7.00 C 16552 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: 1.66 Conformation dependent library (CDL) restraints added in 749.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 975 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 968 " Number of angles added : 12 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5956 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 41 sheets defined 42.5% alpha, 15.7% beta 28 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.941A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.420A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.523A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.661A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.935A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.076A pdb=" N SER C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.674A pdb=" N LEU C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.656A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.831A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.549A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 4.247A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 through 539' Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.023A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.878A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.316A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 removed outlier: 3.556A pdb=" N GLU C 743 " --> pdb=" O ASN C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.858A pdb=" N LEU C 781 " --> pdb=" O SER C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 824 removed outlier: 3.653A pdb=" N ILE C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.655A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 960 through 963 Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 990 through 992 No H-bonds generated for 'chain 'C' and resid 990 through 992' Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 3.794A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.790A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.622A pdb=" N ARG D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.548A pdb=" N PHE D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.623A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.510A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 187 removed outlier: 3.825A pdb=" N ALA D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.566A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.701A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.703A pdb=" N TYR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 357 removed outlier: 3.803A pdb=" N LEU D 357 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.672A pdb=" N ASN D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.550A pdb=" N LEU D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 477 removed outlier: 3.670A pdb=" N ALA D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.079A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.549A pdb=" N THR D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 623 removed outlier: 3.573A pdb=" N ASP D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.742A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 703 removed outlier: 3.526A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.914A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 4.458A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.506A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.669A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 805 " --> pdb=" O THR D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.783A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.703A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 Processing helix chain 'D' and resid 945 through 955 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.758A pdb=" N THR D 967 " --> pdb=" O SER D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 995 through 1005 Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.586A pdb=" N GLN D1009 " --> pdb=" O PRO D1006 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1006 through 1010' Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.730A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.219A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1190 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.584A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.516A pdb=" N VAL D1232 " --> pdb=" O GLU D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 3.572A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 48 through 70 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'F' and resid 83 through 104 removed outlier: 3.808A pdb=" N LEU F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.700A pdb=" N ASP F 111 " --> pdb=" O HIS F 107 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 122 No H-bonds generated for 'chain 'F' and resid 121 through 122' Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 131 through 153 Processing helix chain 'F' and resid 162 through 166 removed outlier: 3.821A pdb=" N VAL F 166 " --> pdb=" O TYR F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 183 through 192 Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.584A pdb=" N ALA F 242 " --> pdb=" O ASP F 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 57 removed outlier: 3.994A pdb=" N VAL M 56 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 147 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.684A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.485A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 3.765A pdb=" N LEU B 14 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 23 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 190 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR B 175 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.961A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 5.939A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 104 through 112 removed outlier: 6.447A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 135 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU M 20 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.750A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 190 removed outlier: 5.008A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.548A pdb=" N MET C 355 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.549A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.728A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.876A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS C 687 " --> pdb=" O ASP C 704 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.820A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.725A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 760 removed outlier: 7.579A pdb=" N ASN C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER C 854 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'C' and resid 801 through 803 removed outlier: 3.527A pdb=" N LEU C 802 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.412A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.954A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD4, first strand: chain 'C' and resid 1133 through 1138 removed outlier: 3.577A pdb=" N ARG D 11 " --> pdb=" O GLU C1136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.674A pdb=" N LYS D 40 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 94 through 102 removed outlier: 10.180A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 900 removed outlier: 4.592A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 902 through 904 Processing sheet with id=AE1, first strand: chain 'D' and resid 1075 through 1077 removed outlier: 4.080A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D1105 " --> pdb=" O GLY D1051 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AE3, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE4, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE5, first strand: chain 'M' and resid 26 through 27 1098 hydrogen bonds defined for protein. 3069 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7549 1.33 - 1.45: 4718 1.45 - 1.57: 14934 1.57 - 1.69: 187 1.69 - 1.81: 156 Bond restraints: 27544 Sorted by residual: bond pdb=" O3' DG H 19 " pdb=" P DT H 20 " ideal model delta sigma weight residual 1.607 1.425 0.182 1.50e-02 4.44e+03 1.48e+02 bond pdb=" C ARG C 282 " pdb=" N PRO C 283 " ideal model delta sigma weight residual 1.333 1.505 -0.172 1.44e-02 4.82e+03 1.42e+02 bond pdb=" O3' DA H 28 " pdb=" P DA H 29 " ideal model delta sigma weight residual 1.607 1.719 -0.112 1.50e-02 4.44e+03 5.61e+01 bond pdb=" C1' DC G 7 " pdb=" N1 DC G 7 " ideal model delta sigma weight residual 1.468 1.561 -0.093 1.40e-02 5.10e+03 4.38e+01 bond pdb=" O3' DG H 33 " pdb=" P DC H 34 " ideal model delta sigma weight residual 1.607 1.698 -0.091 1.50e-02 4.44e+03 3.70e+01 ... (remaining 27539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.58: 37734 7.58 - 15.16: 34 15.16 - 22.74: 2 22.74 - 30.32: 0 30.32 - 37.90: 3 Bond angle restraints: 37773 Sorted by residual: angle pdb=" C3' DT H 31 " pdb=" O3' DT H 31 " pdb=" P DA H 32 " ideal model delta sigma weight residual 120.20 86.58 33.62 1.50e+00 4.44e-01 5.02e+02 angle pdb=" O3' DT H 31 " pdb=" P DA H 32 " pdb=" OP1 DA H 32 " ideal model delta sigma weight residual 108.00 70.10 37.90 3.00e+00 1.11e-01 1.60e+02 angle pdb=" O3' DT H 31 " pdb=" P DA H 32 " pdb=" OP2 DA H 32 " ideal model delta sigma weight residual 108.00 145.20 -37.20 3.00e+00 1.11e-01 1.54e+02 angle pdb=" O2' C I 5 " pdb=" C2' C I 5 " pdb=" C1' C I 5 " ideal model delta sigma weight residual 108.40 92.41 15.99 1.50e+00 4.44e-01 1.14e+02 angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.47 129.86 -10.39 1.16e+00 7.43e-01 8.02e+01 ... (remaining 37768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 16003 35.90 - 71.80: 559 71.80 - 107.70: 20 107.70 - 143.60: 2 143.60 - 179.50: 7 Dihedral angle restraints: 16591 sinusoidal: 7334 harmonic: 9257 Sorted by residual: dihedral pdb=" CA PRO D 322 " pdb=" C PRO D 322 " pdb=" N GLU D 323 " pdb=" CA GLU D 323 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA TRP D 23 " pdb=" C TRP D 23 " pdb=" N SER D 24 " pdb=" CA SER D 24 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" C5' A I 7 " pdb=" C4' A I 7 " pdb=" C3' A I 7 " pdb=" O3' A I 7 " ideal model delta sinusoidal sigma weight residual 147.00 107.58 39.42 1 8.00e+00 1.56e-02 3.41e+01 ... (remaining 16588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4257 0.128 - 0.257: 53 0.257 - 0.385: 7 0.385 - 0.513: 2 0.513 - 0.641: 2 Chirality restraints: 4321 Sorted by residual: chirality pdb=" C3' DG G 25 " pdb=" C4' DG G 25 " pdb=" O3' DG G 25 " pdb=" C2' DG G 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.09 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C3' DC H 24 " pdb=" C4' DC H 24 " pdb=" O3' DC H 24 " pdb=" C2' DC H 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.15 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C3' DT G 17 " pdb=" C4' DT G 17 " pdb=" O3' DT G 17 " pdb=" C2' DT G 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.24 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 4318 not shown) Planarity restraints: 4628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA M 76 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO M 77 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO M 77 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO M 77 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C I 5 " 0.037 2.00e-02 2.50e+03 2.29e-02 1.18e+01 pdb=" N1 C I 5 " -0.056 2.00e-02 2.50e+03 pdb=" C2 C I 5 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C I 5 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C I 5 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C I 5 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C I 5 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C I 5 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C I 5 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 224 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" C THR F 224 " 0.054 2.00e-02 2.50e+03 pdb=" O THR F 224 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL F 225 " -0.018 2.00e-02 2.50e+03 ... (remaining 4625 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 116 2.45 - 3.07: 18069 3.07 - 3.68: 42119 3.68 - 4.29: 57853 4.29 - 4.90: 93649 Nonbonded interactions: 211806 Sorted by model distance: nonbonded pdb=" O3' A I 7 " pdb="MG MG D1401 " model vdw 1.843 2.170 nonbonded pdb=" C2' DA G 19 " pdb=" C7 DT G 20 " model vdw 2.121 3.860 nonbonded pdb=" N4 DC G 2 " pdb=" O6 DG H 47 " model vdw 2.127 3.120 nonbonded pdb=" NZ LYS F 221 " pdb=" C2' DG G 3 " model vdw 2.156 3.520 nonbonded pdb=" NZ LYS F 221 " pdb=" C8 DG G 4 " model vdw 2.180 3.340 ... (remaining 211801 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 88 or (resid 89 through 91 and (name N or name C \ A or name C or name O or name CB )) or resid 92 through 130 or (resid 131 and (n \ ame N or name CA or name C or name O or name CB )) or resid 132 through 223)) selection = (chain 'B' and (resid 5 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 through 185 or (resid 186 and (name N or \ name CA or name C or name O or name CB )) or resid 187 through 223)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.860 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.800 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.005 0.182 27552 Z= 0.316 Angle : 0.826 37.901 37785 Z= 0.499 Chirality : 0.052 0.641 4321 Planarity : 0.004 0.118 4628 Dihedral : 16.997 179.495 10635 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 0.15 % Allowed : 0.42 % Favored : 99.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.27 (0.15), residues: 3212 helix: 1.04 (0.16), residues: 1186 sheet: 0.25 (0.28), residues: 383 loop : -0.42 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 97 TYR 0.014 0.001 TYR E 67 PHE 0.014 0.001 PHE M 71 TRP 0.012 0.001 TRP D 223 HIS 0.009 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.32 (27544) covalent geometry : angle 0.82087 / 0.50 (37773) hydrogen bonds : bond 0.16106 / 10.94 ( 1161) hydrogen bonds : angle 6.63256 / 4.69 ( 3207) metal coordination : bond 0.00920 / 0.44 ( 8) metal coordination : angle 5.38227 / 2.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 376 GLU cc_start: 0.8235 (tm-30) cc_final: 0.8022 (tm-30) REVERT: D 718 ASP cc_start: 0.9071 (t70) cc_final: 0.8800 (t0) REVERT: D 733 MET cc_start: 0.8192 (tmm) cc_final: 0.7888 (tmm) REVERT: D 1112 MET cc_start: 0.8275 (tpt) cc_final: 0.7596 (tpp) REVERT: F 147 MET cc_start: 0.9708 (tmm) cc_final: 0.9259 (tmm) REVERT: F 162 ASP cc_start: 0.8604 (t70) cc_final: 0.8342 (t0) outliers start: 4 outliers final: 2 residues processed: 127 average time/residue: 0.1566 time to fit residues: 33.3961 Evaluate side-chains 98 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain F residue 231 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 175 GLN E 68 ASN F 114 GLN M 72 GLN ** M 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033887 restraints weight = 173536.581| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.79 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27552 Z= 0.139 Angle : 0.617 10.944 37785 Z= 0.327 Chirality : 0.045 0.404 4321 Planarity : 0.005 0.068 4628 Dihedral : 17.503 176.827 4672 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 0.49 % Allowed : 5.81 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: 0.40 (0.15), residues: 3212 helix: 1.24 (0.15), residues: 1193 sheet: 0.18 (0.28), residues: 382 loop : -0.38 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 144 TYR 0.019 0.001 TYR C 91 PHE 0.017 0.001 PHE C 99 TRP 0.011 0.001 TRP M 85 HIS 0.015 0.001 HIS M 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (27544) covalent geometry : angle 0.61155 / 0.33 (37773) hydrogen bonds : bond 0.04947 / 3.45 ( 1161) hydrogen bonds : angle 4.91106 / 3.50 ( 3207) metal coordination : bond 0.00949 / 0.47 ( 8) metal coordination : angle 4.51858 / 2.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9385 (ttp) cc_final: 0.9156 (ppp) REVERT: C 607 MET cc_start: 0.8677 (mtm) cc_final: 0.8455 (mtm) REVERT: D 92 MET cc_start: 0.8629 (mmm) cc_final: 0.6723 (ppp) REVERT: D 155 MET cc_start: 0.8947 (ptm) cc_final: 0.8741 (ptm) REVERT: D 376 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 663 MET cc_start: 0.8869 (tpp) cc_final: 0.8662 (tpp) REVERT: D 718 ASP cc_start: 0.9375 (t70) cc_final: 0.9090 (t0) REVERT: D 733 MET cc_start: 0.8676 (tmm) cc_final: 0.8151 (tmm) REVERT: D 1112 MET cc_start: 0.8317 (tpt) cc_final: 0.7517 (tpp) REVERT: F 147 MET cc_start: 0.9753 (tmm) cc_final: 0.9305 (tmm) REVERT: F 162 ASP cc_start: 0.8595 (t70) cc_final: 0.8338 (t0) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.1502 time to fit residues: 28.4171 Evaluate side-chains 107 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 72 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 146 optimal weight: 0.0770 chunk 64 optimal weight: 30.0000 chunk 196 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 GLN ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.047717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.032860 restraints weight = 174714.357| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 4.76 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27552 Z= 0.188 Angle : 0.598 10.610 37785 Z= 0.318 Chirality : 0.044 0.359 4321 Planarity : 0.004 0.061 4628 Dihedral : 17.440 176.127 4668 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Rotamer: Outliers : 0.68 % Allowed : 8.55 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: 0.51 (0.15), residues: 3212 helix: 1.43 (0.15), residues: 1193 sheet: 0.12 (0.27), residues: 389 loop : -0.38 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 144 TYR 0.019 0.001 TYR F 177 PHE 0.020 0.001 PHE M 71 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (27544) covalent geometry : angle 0.59397 / 0.32 (37773) hydrogen bonds : bond 0.04496 / 3.12 ( 1161) hydrogen bonds : angle 4.67287 / 3.34 ( 3207) metal coordination : bond 0.01335 / 0.66 ( 8) metal coordination : angle 4.11328 / 2.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9407 (ttp) cc_final: 0.9176 (ppp) REVERT: C 607 MET cc_start: 0.8803 (mtm) cc_final: 0.8496 (mtm) REVERT: D 92 MET cc_start: 0.8694 (mmm) cc_final: 0.6844 (ppp) REVERT: D 205 MET cc_start: 0.7777 (mmm) cc_final: 0.7572 (mmm) REVERT: D 376 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 663 MET cc_start: 0.8831 (tpp) cc_final: 0.8533 (tpp) REVERT: D 718 ASP cc_start: 0.9416 (t70) cc_final: 0.9113 (t0) REVERT: D 733 MET cc_start: 0.8728 (tmm) cc_final: 0.8198 (tmm) REVERT: D 1112 MET cc_start: 0.8413 (tpt) cc_final: 0.7319 (tpt) REVERT: F 147 MET cc_start: 0.9764 (tmm) cc_final: 0.9345 (tmm) REVERT: F 162 ASP cc_start: 0.8669 (t70) cc_final: 0.8397 (t0) outliers start: 18 outliers final: 10 residues processed: 113 average time/residue: 0.1347 time to fit residues: 26.8250 Evaluate side-chains 109 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 60 optimal weight: 8.9990 chunk 107 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 0.0570 chunk 308 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 196 optimal weight: 0.2980 chunk 243 optimal weight: 6.9990 chunk 262 optimal weight: 20.0000 overall best weight: 1.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.048251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.033435 restraints weight = 172558.828| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 4.76 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27552 Z= 0.117 Angle : 0.553 11.743 37785 Z= 0.294 Chirality : 0.043 0.365 4321 Planarity : 0.004 0.061 4628 Dihedral : 17.359 175.383 4664 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 0.68 % Allowed : 10.64 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3212 helix: 1.53 (0.15), residues: 1200 sheet: 0.22 (0.28), residues: 382 loop : -0.34 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.021 0.001 TYR C 91 PHE 0.010 0.001 PHE C 153 TRP 0.010 0.001 TRP C 938 HIS 0.003 0.001 HIS C 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (27544) covalent geometry : angle 0.54943 / 0.29 (37773) hydrogen bonds : bond 0.03983 / 2.76 ( 1161) hydrogen bonds : angle 4.46649 / 3.20 ( 3207) metal coordination : bond 0.00792 / 0.39 ( 8) metal coordination : angle 3.57142 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9435 (ttp) cc_final: 0.9233 (ppp) REVERT: D 92 MET cc_start: 0.8747 (mmm) cc_final: 0.6852 (ppp) REVERT: D 205 MET cc_start: 0.7735 (mmm) cc_final: 0.7499 (mmt) REVERT: D 252 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: D 376 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8415 (tm-30) REVERT: D 541 MET cc_start: 0.8549 (mmm) cc_final: 0.8117 (mmm) REVERT: D 666 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9060 (p) REVERT: D 718 ASP cc_start: 0.9385 (t70) cc_final: 0.9080 (t0) REVERT: D 733 MET cc_start: 0.8728 (tmm) cc_final: 0.8191 (tmm) REVERT: D 1112 MET cc_start: 0.8433 (tpt) cc_final: 0.7711 (tpp) REVERT: F 147 MET cc_start: 0.9758 (tmm) cc_final: 0.9341 (tmm) REVERT: F 162 ASP cc_start: 0.8682 (t70) cc_final: 0.8405 (t0) outliers start: 18 outliers final: 6 residues processed: 116 average time/residue: 0.1418 time to fit residues: 28.6316 Evaluate side-chains 107 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1208 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 284 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 324 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 276 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN F 114 GLN M 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.046257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.031459 restraints weight = 175105.692| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 4.70 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 27552 Z= 0.293 Angle : 0.678 12.595 37785 Z= 0.353 Chirality : 0.045 0.345 4321 Planarity : 0.005 0.060 4628 Dihedral : 17.381 173.729 4664 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 1.44 % Allowed : 12.27 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: 0.42 (0.15), residues: 3212 helix: 1.38 (0.15), residues: 1207 sheet: -0.03 (0.27), residues: 378 loop : -0.44 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.018 0.002 TYR C 91 PHE 0.016 0.002 PHE C 373 TRP 0.016 0.001 TRP D 723 HIS 0.007 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.29 (27544) covalent geometry : angle 0.67327 / 0.35 (37773) hydrogen bonds : bond 0.04989 / 3.47 ( 1161) hydrogen bonds : angle 4.72157 / 3.37 ( 3207) metal coordination : bond 0.01945 / 0.97 ( 8) metal coordination : angle 4.73403 / 2.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9411 (ttp) cc_final: 0.9173 (ppp) REVERT: C 159 MET cc_start: 0.8912 (mmm) cc_final: 0.8325 (mpp) REVERT: D 92 MET cc_start: 0.8757 (mmm) cc_final: 0.6988 (ppp) REVERT: D 205 MET cc_start: 0.7796 (mmm) cc_final: 0.7548 (mmt) REVERT: D 252 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: D 376 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 666 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9172 (p) REVERT: D 718 ASP cc_start: 0.9438 (t70) cc_final: 0.9139 (t0) REVERT: D 733 MET cc_start: 0.8798 (tmm) cc_final: 0.8283 (tmm) REVERT: D 1112 MET cc_start: 0.8352 (tpt) cc_final: 0.8076 (tpt) REVERT: F 147 MET cc_start: 0.9777 (tmm) cc_final: 0.9407 (tmm) REVERT: F 162 ASP cc_start: 0.8666 (t70) cc_final: 0.8398 (t0) outliers start: 38 outliers final: 19 residues processed: 126 average time/residue: 0.1401 time to fit residues: 30.8949 Evaluate side-chains 120 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 186 optimal weight: 0.1980 chunk 8 optimal weight: 9.9990 chunk 323 optimal weight: 50.0000 chunk 163 optimal weight: 2.9990 chunk 304 optimal weight: 40.0000 chunk 269 optimal weight: 7.9990 chunk 324 optimal weight: 30.0000 chunk 289 optimal weight: 0.0070 chunk 203 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.047083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.032224 restraints weight = 173273.402| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 4.74 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27552 Z= 0.143 Angle : 0.575 12.559 37785 Z= 0.303 Chirality : 0.043 0.350 4321 Planarity : 0.004 0.060 4628 Dihedral : 17.318 174.569 4664 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.37 % Allowed : 13.22 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3212 helix: 1.60 (0.15), residues: 1199 sheet: 0.13 (0.27), residues: 385 loop : -0.44 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 325 TYR 0.032 0.001 TYR D 344 PHE 0.009 0.001 PHE C 153 TRP 0.013 0.001 TRP D 723 HIS 0.004 0.001 HIS C 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (27544) covalent geometry : angle 0.57093 / 0.30 (37773) hydrogen bonds : bond 0.04179 / 2.90 ( 1161) hydrogen bonds : angle 4.46117 / 3.19 ( 3207) metal coordination : bond 0.01016 / 0.50 ( 8) metal coordination : angle 3.85327 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9447 (ttp) cc_final: 0.9182 (ppp) REVERT: C 159 MET cc_start: 0.8909 (mmm) cc_final: 0.8226 (mpp) REVERT: C 607 MET cc_start: 0.8862 (mtm) cc_final: 0.8601 (mtm) REVERT: D 92 MET cc_start: 0.8825 (mmm) cc_final: 0.7029 (ppp) REVERT: D 205 MET cc_start: 0.7866 (mmm) cc_final: 0.7613 (mmt) REVERT: D 252 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8300 (m-10) REVERT: D 327 MET cc_start: 0.8377 (tpt) cc_final: 0.8092 (tpt) REVERT: D 376 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 666 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9159 (p) REVERT: D 718 ASP cc_start: 0.9429 (t70) cc_final: 0.9153 (t0) REVERT: D 733 MET cc_start: 0.8783 (tmm) cc_final: 0.8264 (tmm) REVERT: D 983 MET cc_start: 0.9076 (mmm) cc_final: 0.8518 (tmm) REVERT: D 1112 MET cc_start: 0.8401 (tpt) cc_final: 0.8106 (tpt) REVERT: F 147 MET cc_start: 0.9782 (tmm) cc_final: 0.9368 (tmm) REVERT: F 162 ASP cc_start: 0.8649 (t70) cc_final: 0.8307 (t0) outliers start: 36 outliers final: 20 residues processed: 132 average time/residue: 0.1387 time to fit residues: 31.9826 Evaluate side-chains 123 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 257 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.046840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031994 restraints weight = 173240.368| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.72 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27552 Z= 0.178 Angle : 0.589 10.812 37785 Z= 0.309 Chirality : 0.043 0.341 4321 Planarity : 0.004 0.059 4628 Dihedral : 17.279 173.944 4664 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 1.44 % Allowed : 13.72 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3212 helix: 1.59 (0.15), residues: 1202 sheet: 0.04 (0.27), residues: 395 loop : -0.45 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 165 TYR 0.020 0.001 TYR C 91 PHE 0.010 0.001 PHE C 300 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (27544) covalent geometry : angle 0.58550 / 0.31 (37773) hydrogen bonds : bond 0.04160 / 2.87 ( 1161) hydrogen bonds : angle 4.43937 / 3.18 ( 3207) metal coordination : bond 0.01199 / 0.60 ( 8) metal coordination : angle 3.88365 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9458 (ttp) cc_final: 0.9224 (ppp) REVERT: C 159 MET cc_start: 0.8891 (mmm) cc_final: 0.8325 (mpp) REVERT: C 607 MET cc_start: 0.8870 (mtm) cc_final: 0.8630 (mtm) REVERT: D 92 MET cc_start: 0.8857 (mmm) cc_final: 0.7080 (ppp) REVERT: D 205 MET cc_start: 0.7912 (mmm) cc_final: 0.7658 (mmt) REVERT: D 252 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8365 (m-10) REVERT: D 376 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8428 (tm-30) REVERT: D 666 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9180 (p) REVERT: D 718 ASP cc_start: 0.9421 (t70) cc_final: 0.9149 (t0) REVERT: D 733 MET cc_start: 0.8798 (tmm) cc_final: 0.8290 (tmm) REVERT: D 983 MET cc_start: 0.9192 (mmm) cc_final: 0.8477 (tmm) REVERT: D 1112 MET cc_start: 0.8417 (tpt) cc_final: 0.7570 (tpt) REVERT: F 147 MET cc_start: 0.9781 (tmm) cc_final: 0.9369 (tmm) REVERT: F 162 ASP cc_start: 0.8585 (t70) cc_final: 0.8316 (t0) outliers start: 38 outliers final: 23 residues processed: 135 average time/residue: 0.1422 time to fit residues: 32.8044 Evaluate side-chains 125 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 10 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 174 optimal weight: 50.0000 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 288 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.046366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.031508 restraints weight = 176373.961| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 4.71 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27552 Z= 0.213 Angle : 0.617 11.030 37785 Z= 0.322 Chirality : 0.044 0.335 4321 Planarity : 0.004 0.059 4628 Dihedral : 17.277 173.516 4664 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 1.52 % Allowed : 13.94 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3212 helix: 1.55 (0.15), residues: 1201 sheet: 0.01 (0.26), residues: 405 loop : -0.54 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1044 TYR 0.023 0.001 TYR C 91 PHE 0.010 0.001 PHE F 121 TRP 0.013 0.001 TRP D 723 HIS 0.005 0.001 HIS C 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (27544) covalent geometry : angle 0.61272 / 0.32 (37773) hydrogen bonds : bond 0.04336 / 2.99 ( 1161) hydrogen bonds : angle 4.49634 / 3.21 ( 3207) metal coordination : bond 0.01411 / 0.70 ( 8) metal coordination : angle 4.11511 / 2.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9454 (ttp) cc_final: 0.9218 (ppp) REVERT: C 159 MET cc_start: 0.8891 (mmm) cc_final: 0.8307 (mpp) REVERT: C 607 MET cc_start: 0.8890 (mtm) cc_final: 0.8635 (mtm) REVERT: D 92 MET cc_start: 0.8870 (mmm) cc_final: 0.7163 (ppp) REVERT: D 205 MET cc_start: 0.7958 (mmm) cc_final: 0.7705 (mmt) REVERT: D 252 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8452 (m-10) REVERT: D 376 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8450 (tm-30) REVERT: D 666 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9219 (p) REVERT: D 718 ASP cc_start: 0.9419 (t70) cc_final: 0.9139 (t0) REVERT: D 733 MET cc_start: 0.8809 (tmm) cc_final: 0.8303 (tmm) REVERT: F 147 MET cc_start: 0.9784 (tmm) cc_final: 0.9425 (tmm) REVERT: F 162 ASP cc_start: 0.8614 (t70) cc_final: 0.8344 (t0) outliers start: 40 outliers final: 30 residues processed: 130 average time/residue: 0.1484 time to fit residues: 33.8314 Evaluate side-chains 130 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 19 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 175 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.031806 restraints weight = 174366.909| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 4.72 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27552 Z= 0.160 Angle : 0.586 10.404 37785 Z= 0.305 Chirality : 0.043 0.337 4321 Planarity : 0.004 0.059 4628 Dihedral : 17.248 173.370 4664 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.52 % Allowed : 14.29 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.55 (0.15), residues: 3212 helix: 1.62 (0.15), residues: 1203 sheet: 0.07 (0.27), residues: 405 loop : -0.50 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 325 TYR 0.022 0.001 TYR C 91 PHE 0.010 0.001 PHE C 153 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (27544) covalent geometry : angle 0.58198 / 0.30 (37773) hydrogen bonds : bond 0.04022 / 2.76 ( 1161) hydrogen bonds : angle 4.38038 / 3.13 ( 3207) metal coordination : bond 0.01080 / 0.54 ( 8) metal coordination : angle 4.04718 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9463 (ttp) cc_final: 0.9239 (ppp) REVERT: C 159 MET cc_start: 0.8879 (mmm) cc_final: 0.8651 (tpp) REVERT: C 607 MET cc_start: 0.8866 (mtm) cc_final: 0.8458 (mtm) REVERT: C 611 MET cc_start: 0.9177 (mtm) cc_final: 0.8834 (mtm) REVERT: D 92 MET cc_start: 0.8892 (mmm) cc_final: 0.7163 (ppp) REVERT: D 205 MET cc_start: 0.7947 (mmm) cc_final: 0.7693 (mmt) REVERT: D 252 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8362 (m-10) REVERT: D 376 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 666 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9226 (p) REVERT: D 718 ASP cc_start: 0.9428 (t70) cc_final: 0.9159 (t0) REVERT: D 733 MET cc_start: 0.8808 (tmm) cc_final: 0.8258 (tmm) REVERT: D 1112 MET cc_start: 0.8205 (tpt) cc_final: 0.7922 (tpt) REVERT: F 147 MET cc_start: 0.9788 (tmm) cc_final: 0.9380 (tmm) REVERT: F 162 ASP cc_start: 0.8586 (t70) cc_final: 0.8318 (t0) outliers start: 40 outliers final: 32 residues processed: 136 average time/residue: 0.1512 time to fit residues: 36.6416 Evaluate side-chains 135 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 323 optimal weight: 50.0000 chunk 287 optimal weight: 20.0000 chunk 318 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.046215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.031366 restraints weight = 175557.161| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 4.69 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27552 Z= 0.224 Angle : 0.627 12.743 37785 Z= 0.326 Chirality : 0.044 0.332 4321 Planarity : 0.004 0.059 4628 Dihedral : 17.264 172.977 4664 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.48 % Allowed : 14.70 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.49 (0.15), residues: 3212 helix: 1.60 (0.15), residues: 1204 sheet: 0.02 (0.27), residues: 405 loop : -0.55 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 667 TYR 0.024 0.001 TYR C 91 PHE 0.011 0.001 PHE F 121 TRP 0.039 0.001 TRP D 223 HIS 0.005 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (27544) covalent geometry : angle 0.62259 / 0.33 (37773) hydrogen bonds : bond 0.04278 / 2.94 ( 1161) hydrogen bonds : angle 4.48197 / 3.19 ( 3207) metal coordination : bond 0.01463 / 0.73 ( 8) metal coordination : angle 4.18119 / 2.11 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9445 (ttp) cc_final: 0.9219 (ppp) REVERT: C 159 MET cc_start: 0.8885 (mmm) cc_final: 0.8273 (mpp) REVERT: C 607 MET cc_start: 0.8876 (mtm) cc_final: 0.8593 (mtm) REVERT: D 92 MET cc_start: 0.8848 (mmm) cc_final: 0.7139 (ppp) REVERT: D 205 MET cc_start: 0.7912 (mmm) cc_final: 0.7656 (mmt) REVERT: D 252 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8444 (m-10) REVERT: D 373 MET cc_start: 0.8463 (ptt) cc_final: 0.8168 (ptt) REVERT: D 376 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 581 MET cc_start: 0.9288 (mtm) cc_final: 0.8912 (mtm) REVERT: D 666 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9220 (p) REVERT: D 718 ASP cc_start: 0.9413 (t70) cc_final: 0.9149 (t0) REVERT: D 733 MET cc_start: 0.8842 (tmm) cc_final: 0.8321 (tmm) REVERT: D 1112 MET cc_start: 0.8126 (tpt) cc_final: 0.7813 (tpt) REVERT: F 147 MET cc_start: 0.9786 (tmm) cc_final: 0.9432 (tmm) REVERT: F 162 ASP cc_start: 0.8606 (t70) cc_final: 0.8335 (t0) outliers start: 39 outliers final: 31 residues processed: 131 average time/residue: 0.1529 time to fit residues: 34.9166 Evaluate side-chains 130 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 121 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 291 optimal weight: 7.9990 chunk 200 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.047074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.032251 restraints weight = 171778.174| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 4.70 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27552 Z= 0.120 Angle : 0.580 10.990 37785 Z= 0.301 Chirality : 0.043 0.337 4321 Planarity : 0.004 0.058 4628 Dihedral : 17.208 173.105 4664 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.22 % Allowed : 15.12 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: 0.63 (0.15), residues: 3212 helix: 1.69 (0.16), residues: 1204 sheet: 0.19 (0.27), residues: 392 loop : -0.48 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 395 TYR 0.024 0.001 TYR C 91 PHE 0.011 0.001 PHE C 153 TRP 0.033 0.001 TRP D 223 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (27544) covalent geometry : angle 0.57556 / 0.30 (37773) hydrogen bonds : bond 0.03762 / 2.58 ( 1161) hydrogen bonds : angle 4.30019 / 3.07 ( 3207) metal coordination : bond 0.00782 / 0.39 ( 8) metal coordination : angle 4.01515 / 2.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4411.14 seconds wall clock time: 76 minutes 48.10 seconds (4608.10 seconds total)