Starting phenix.real_space_refine on Fri Feb 6 19:31:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m98_63729/02_2026/9m98_63729_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m98_63729/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9m98_63729/02_2026/9m98_63729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m98_63729/02_2026/9m98_63729.map" model { file = "/net/cci-nas-00/data/ceres_data/9m98_63729/02_2026/9m98_63729_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m98_63729/02_2026/9m98_63729_neut.cif" } 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-2.0-5952/lib/python3.9/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: 5.11, per 1000 atoms: 0.19 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: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.21 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: 5.67 Time building geometry restraints manager: 3.12 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=" 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 bond pdb=" O3' DT G 14 " pdb=" P DG G 15 " ideal model delta sigma weight residual 1.607 1.684 -0.077 1.50e-02 4.44e+03 2.62e+01 ... (remaining 27539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.58: 37737 7.58 - 15.16: 31 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=" O3' DT H 43 " pdb=" C3' DT H 43 " pdb=" C2' DT H 43 " ideal model delta sigma weight residual 111.50 93.38 18.12 1.50e+00 4.44e-01 1.46e+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 ... (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 - 0.114: 4221 0.114 - 0.228: 79 0.228 - 0.343: 16 0.343 - 0.457: 3 0.457 - 0.571: 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 -2.66 -2.09 -0.57 2.00e-01 2.50e+01 8.15e+00 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 -2.66 -2.15 -0.51 2.00e-01 2.50e+01 6.53e+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 -2.66 -2.24 -0.42 2.00e-01 2.50e+01 4.34e+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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 27.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 27552 Z= 0.236 Angle : 0.824 37.901 37785 Z= 0.471 Chirality : 0.050 0.571 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 covalent geometry : bond 0.00441 (27544) covalent geometry : angle 0.81842 (37773) hydrogen bonds : bond 0.16106 ( 1161) hydrogen bonds : angle 6.63256 ( 3207) metal coordination : bond 0.00920 ( 8) metal coordination : angle 5.38227 ( 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 : 1.024 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: 0.1579 time to fit residues: 34.0620 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 : 0.732 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 981 GLN D 175 GLN E 68 ASN E 87 GLN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN M 78 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.033884 restraints weight = 173636.123| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.80 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 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 = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27552 Z= 0.137 Angle : 0.587 9.890 37785 Z= 0.308 Chirality : 0.043 0.216 4321 Planarity : 0.004 0.073 4628 Dihedral : 17.487 177.978 4672 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 0.49 % Allowed : 6.04 % Favored : 93.47 % 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: 0.48 (0.15), residues: 3212 helix: 1.33 (0.16), residues: 1192 sheet: 0.25 (0.28), residues: 381 loop : -0.37 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 97 TYR 0.019 0.001 TYR C 91 PHE 0.012 0.001 PHE C 153 TRP 0.009 0.001 TRP M 85 HIS 0.015 0.001 HIS M 78 Details of bonding type rmsd covalent geometry : bond 0.00303 (27544) covalent geometry : angle 0.58128 (37773) hydrogen bonds : bond 0.04499 ( 1161) hydrogen bonds : angle 4.76168 ( 3207) metal coordination : bond 0.00927 ( 8) metal coordination : angle 4.50285 ( 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 119 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 607 MET cc_start: 0.8662 (mtm) cc_final: 0.8363 (mtm) REVERT: D 92 MET cc_start: 0.8714 (mmm) cc_final: 0.6787 (ppp) REVERT: D 155 MET cc_start: 0.9020 (ptm) cc_final: 0.8814 (ptm) REVERT: D 373 MET cc_start: 0.8422 (mtm) cc_final: 0.8104 (mtt) REVERT: D 376 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8342 (tm-30) REVERT: D 718 ASP cc_start: 0.9373 (t70) cc_final: 0.9090 (t0) REVERT: D 733 MET cc_start: 0.8711 (tmm) cc_final: 0.8200 (tmm) REVERT: D 1112 MET cc_start: 0.8307 (tpt) cc_final: 0.7491 (tpp) REVERT: F 147 MET cc_start: 0.9743 (tmm) cc_final: 0.9320 (tmm) REVERT: F 162 ASP cc_start: 0.8666 (t70) cc_final: 0.8394 (t0) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.1642 time to fit residues: 31.6760 Evaluate side-chains 108 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 737 LEU 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 72 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 146 optimal weight: 0.0980 chunk 64 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 296 optimal weight: 0.0980 chunk 138 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 245 optimal weight: 0.7980 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.047799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032965 restraints weight = 174712.377| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 4.76 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27552 Z= 0.168 Angle : 0.574 10.289 37785 Z= 0.301 Chirality : 0.042 0.201 4321 Planarity : 0.004 0.126 4628 Dihedral : 17.384 178.497 4664 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.01 % Rotamer: Outliers : 0.61 % Allowed : 9.23 % Favored : 90.16 % 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: 0.55 (0.15), residues: 3212 helix: 1.44 (0.15), residues: 1201 sheet: 0.20 (0.27), residues: 386 loop : -0.37 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 282 TYR 0.020 0.001 TYR C 91 PHE 0.011 0.001 PHE C 373 TRP 0.012 0.001 TRP D 723 HIS 0.004 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00376 (27544) covalent geometry : angle 0.56978 (37773) hydrogen bonds : bond 0.04156 ( 1161) hydrogen bonds : angle 4.52779 ( 3207) metal coordination : bond 0.01149 ( 8) metal coordination : angle 4.14635 ( 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: 16 poor density : 103 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 MET cc_start: 0.9269 (mmm) cc_final: 0.9067 (tpp) REVERT: C 159 MET cc_start: 0.8956 (mmm) cc_final: 0.8271 (mpp) REVERT: C 607 MET cc_start: 0.8752 (mtm) cc_final: 0.8458 (mtm) REVERT: D 92 MET cc_start: 0.8732 (mmm) cc_final: 0.6836 (ppp) REVERT: D 205 MET cc_start: 0.7718 (mmm) cc_final: 0.7498 (mmt) REVERT: D 373 MET cc_start: 0.8415 (mtm) cc_final: 0.7957 (mtt) REVERT: D 376 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 718 ASP cc_start: 0.9411 (t70) cc_final: 0.9123 (t0) REVERT: D 733 MET cc_start: 0.8738 (tmm) cc_final: 0.8208 (tmm) REVERT: D 1112 MET cc_start: 0.8419 (tpt) cc_final: 0.7348 (tpt) REVERT: F 147 MET cc_start: 0.9767 (tmm) cc_final: 0.9347 (tmm) REVERT: F 162 ASP cc_start: 0.8672 (t70) cc_final: 0.8391 (t0) outliers start: 16 outliers final: 9 residues processed: 116 average time/residue: 0.1419 time to fit residues: 29.0210 Evaluate side-chains 106 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 470 LEU 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 381 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 60 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 308 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 262 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 87 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.046652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.031834 restraints weight = 174949.978| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 4.72 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27552 Z= 0.229 Angle : 0.608 13.226 37785 Z= 0.318 Chirality : 0.043 0.249 4321 Planarity : 0.004 0.081 4628 Dihedral : 17.422 178.327 4664 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 1.33 % Allowed : 11.02 % Favored : 87.65 % 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: 0.51 (0.15), residues: 3212 helix: 1.42 (0.15), residues: 1212 sheet: 0.19 (0.27), residues: 391 loop : -0.42 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 282 TYR 0.021 0.001 TYR C 91 PHE 0.013 0.001 PHE C 373 TRP 0.014 0.001 TRP D 723 HIS 0.005 0.001 HIS C 662 Details of bonding type rmsd covalent geometry : bond 0.00515 (27544) covalent geometry : angle 0.60340 (37773) hydrogen bonds : bond 0.04442 ( 1161) hydrogen bonds : angle 4.57209 ( 3207) metal coordination : bond 0.01455 ( 8) metal coordination : angle 4.37518 ( 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 137 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 HIS cc_start: 0.9297 (OUTLIER) cc_final: 0.9072 (t-170) REVERT: C 154 MET cc_start: 0.9274 (mmm) cc_final: 0.8948 (tpp) REVERT: C 607 MET cc_start: 0.8833 (mtm) cc_final: 0.8486 (mtm) REVERT: D 92 MET cc_start: 0.8814 (mmm) cc_final: 0.7005 (ppp) REVERT: D 205 MET cc_start: 0.7733 (mmm) cc_final: 0.7512 (mmm) REVERT: D 252 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8361 (m-10) REVERT: D 376 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8390 (tm-30) REVERT: D 666 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9175 (p) REVERT: D 718 ASP cc_start: 0.9429 (t70) cc_final: 0.9155 (t0) REVERT: D 733 MET cc_start: 0.8791 (tmm) cc_final: 0.8264 (tmm) REVERT: D 1112 MET cc_start: 0.8427 (tpt) cc_final: 0.8153 (tpt) REVERT: F 147 MET cc_start: 0.9776 (tmm) cc_final: 0.9411 (tmm) REVERT: F 162 ASP cc_start: 0.8645 (t70) cc_final: 0.8317 (t0) outliers start: 35 outliers final: 14 residues processed: 128 average time/residue: 0.1424 time to fit residues: 31.8696 Evaluate side-chains 117 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 124 HIS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 284 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3264 r_free = 0.3264 target = 0.046688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031885 restraints weight = 174200.386| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 4.70 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27552 Z= 0.189 Angle : 0.583 11.784 37785 Z= 0.303 Chirality : 0.042 0.240 4321 Planarity : 0.004 0.058 4628 Dihedral : 17.376 177.976 4664 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.67 % Allowed : 12.31 % Favored : 86.02 % 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 (0.16), residues: 1201 sheet: 0.14 (0.27), residues: 393 loop : -0.47 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 109 TYR 0.028 0.001 TYR D 344 PHE 0.009 0.001 PHE C 153 TRP 0.012 0.001 TRP D 723 HIS 0.003 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00424 (27544) covalent geometry : angle 0.57852 (37773) hydrogen bonds : bond 0.04022 ( 1161) hydrogen bonds : angle 4.42854 ( 3207) metal coordination : bond 0.01248 ( 8) metal coordination : angle 3.97393 ( 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 147 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 607 MET cc_start: 0.8840 (mtm) cc_final: 0.8503 (mtm) REVERT: D 92 MET cc_start: 0.8866 (mmm) cc_final: 0.7039 (ppp) REVERT: D 205 MET cc_start: 0.7856 (mmm) cc_final: 0.7629 (mmt) REVERT: D 376 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 418 LEU cc_start: 0.9046 (mt) cc_final: 0.8770 (mp) REVERT: D 581 MET cc_start: 0.8911 (mtp) cc_final: 0.8709 (mtm) REVERT: D 666 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9230 (p) REVERT: D 718 ASP cc_start: 0.9425 (t70) cc_final: 0.9158 (t0) REVERT: D 733 MET cc_start: 0.8809 (tmm) cc_final: 0.8304 (tmm) REVERT: D 983 MET cc_start: 0.8972 (mmm) cc_final: 0.8750 (mmm) REVERT: D 1112 MET cc_start: 0.8455 (tpt) cc_final: 0.7650 (tpt) REVERT: F 147 MET cc_start: 0.9781 (tmm) cc_final: 0.9409 (tmm) REVERT: F 162 ASP cc_start: 0.8618 (t70) cc_final: 0.8351 (t0) outliers start: 44 outliers final: 25 residues processed: 139 average time/residue: 0.1332 time to fit residues: 32.7214 Evaluate side-chains 127 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 470 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 186 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 chunk 304 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 289 optimal weight: 0.0670 chunk 203 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** 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 = 0.3278 r_free = 0.3278 target = 0.047147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.032271 restraints weight = 172576.888| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 4.73 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27552 Z= 0.133 Angle : 0.556 12.488 37785 Z= 0.288 Chirality : 0.042 0.219 4321 Planarity : 0.004 0.056 4628 Dihedral : 17.313 176.802 4664 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.60 % Allowed : 12.84 % Favored : 85.56 % 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: 0.65 (0.15), residues: 3212 helix: 1.69 (0.16), residues: 1203 sheet: 0.22 (0.27), residues: 396 loop : -0.46 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 870 TYR 0.022 0.001 TYR C 91 PHE 0.010 0.001 PHE C 153 TRP 0.010 0.001 TRP D 723 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00298 (27544) covalent geometry : angle 0.55261 (37773) hydrogen bonds : bond 0.03679 ( 1161) hydrogen bonds : angle 4.27983 ( 3207) metal coordination : bond 0.00899 ( 8) metal coordination : angle 3.70041 ( 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 147 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.9356 (ptp) cc_final: 0.9050 (mpp) REVERT: C 607 MET cc_start: 0.8803 (mtm) cc_final: 0.8499 (mtm) REVERT: D 92 MET cc_start: 0.8809 (mmm) cc_final: 0.7061 (ppp) REVERT: D 205 MET cc_start: 0.7862 (mmm) cc_final: 0.7611 (mmt) REVERT: D 252 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: D 373 MET cc_start: 0.8542 (mtm) cc_final: 0.8328 (mtm) REVERT: D 376 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 418 LEU cc_start: 0.9015 (mt) cc_final: 0.8736 (mp) REVERT: D 666 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9244 (p) REVERT: D 718 ASP cc_start: 0.9419 (t70) cc_final: 0.9159 (t0) REVERT: D 733 MET cc_start: 0.8812 (tmm) cc_final: 0.8301 (tmm) REVERT: F 116 THR cc_start: 0.9453 (m) cc_final: 0.9150 (p) REVERT: F 147 MET cc_start: 0.9781 (tmm) cc_final: 0.9372 (tmm) REVERT: F 162 ASP cc_start: 0.8673 (t70) cc_final: 0.8402 (t0) outliers start: 42 outliers final: 24 residues processed: 138 average time/residue: 0.1551 time to fit residues: 37.5139 Evaluate side-chains 129 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 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 381 LEU Chi-restraints excluded: chain D residue 402 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 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain M residue 46 VAL 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: 10.0000 chunk 246 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 71 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3260 r_free = 0.3260 target = 0.046516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031687 restraints weight = 172772.708| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 4.68 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27552 Z= 0.189 Angle : 0.588 9.797 37785 Z= 0.304 Chirality : 0.042 0.222 4321 Planarity : 0.004 0.053 4628 Dihedral : 17.344 176.665 4664 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 2.01 % Allowed : 13.72 % Favored : 84.27 % 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: 0.61 (0.15), residues: 3212 helix: 1.68 (0.16), residues: 1205 sheet: 0.17 (0.27), residues: 397 loop : -0.50 (0.16), residues: 1610 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 0.013 0.001 PHE F 117 TRP 0.011 0.001 TRP D 723 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00425 (27544) covalent geometry : angle 0.58391 (37773) hydrogen bonds : bond 0.04024 ( 1161) hydrogen bonds : angle 4.34757 ( 3207) metal coordination : bond 0.01258 ( 8) metal coordination : angle 3.91037 ( 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 154 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.9326 (ptp) cc_final: 0.9026 (mpp) REVERT: C 607 MET cc_start: 0.8813 (mtm) cc_final: 0.8543 (mtm) REVERT: D 92 MET cc_start: 0.8803 (mmm) cc_final: 0.7195 (ppp) REVERT: D 205 MET cc_start: 0.7852 (mmm) cc_final: 0.7582 (mmm) REVERT: D 252 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (m-10) REVERT: D 376 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 418 LEU cc_start: 0.9014 (mt) cc_final: 0.8732 (mp) REVERT: D 581 MET cc_start: 0.8848 (mtp) cc_final: 0.8636 (mtm) REVERT: D 666 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9241 (p) REVERT: D 718 ASP cc_start: 0.9419 (t70) cc_final: 0.9148 (t0) REVERT: D 733 MET cc_start: 0.8842 (tmm) cc_final: 0.8320 (tmm) REVERT: D 983 MET cc_start: 0.8945 (mmm) cc_final: 0.8679 (mmm) REVERT: D 1112 MET cc_start: 0.8099 (tpt) cc_final: 0.7759 (tpt) REVERT: F 147 MET cc_start: 0.9783 (tmm) cc_final: 0.9427 (tmm) REVERT: F 162 ASP cc_start: 0.8682 (t70) cc_final: 0.8417 (t0) outliers start: 53 outliers final: 31 residues processed: 147 average time/residue: 0.1541 time to fit residues: 39.1456 Evaluate side-chains 134 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 424 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 989 LEU 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 E residue 67 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 174 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3250 r_free = 0.3250 target = 0.046245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.031372 restraints weight = 176304.916| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 4.72 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 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 = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27552 Z= 0.208 Angle : 0.606 14.652 37785 Z= 0.312 Chirality : 0.042 0.260 4321 Planarity : 0.004 0.051 4628 Dihedral : 17.403 176.798 4664 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.52 % Allowed : 14.55 % Favored : 83.93 % 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: 0.57 (0.15), residues: 3212 helix: 1.69 (0.16), residues: 1203 sheet: 0.13 (0.27), residues: 397 loop : -0.54 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.023 0.001 TYR C 91 PHE 0.014 0.001 PHE C 300 TRP 0.029 0.001 TRP D 223 HIS 0.006 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00465 (27544) covalent geometry : angle 0.60124 (37773) hydrogen bonds : bond 0.04096 ( 1161) hydrogen bonds : angle 4.38745 ( 3207) metal coordination : bond 0.01350 ( 8) metal coordination : angle 4.09908 ( 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 137 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 607 MET cc_start: 0.8848 (mtm) cc_final: 0.8561 (mtm) REVERT: D 92 MET cc_start: 0.8812 (mmm) cc_final: 0.7209 (ppp) REVERT: D 205 MET cc_start: 0.7899 (mmm) cc_final: 0.7637 (mmm) REVERT: D 252 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: D 376 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 457 MET cc_start: 0.9261 (tpp) cc_final: 0.9043 (mmt) REVERT: D 581 MET cc_start: 0.8974 (mtp) cc_final: 0.8750 (mtm) REVERT: D 666 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9245 (p) REVERT: D 718 ASP cc_start: 0.9409 (t70) cc_final: 0.9148 (t0) REVERT: D 733 MET cc_start: 0.8851 (tmm) cc_final: 0.8331 (tmm) REVERT: D 983 MET cc_start: 0.9028 (mmm) cc_final: 0.8578 (mmm) REVERT: D 1112 MET cc_start: 0.8195 (tpt) cc_final: 0.7264 (tpt) REVERT: F 147 MET cc_start: 0.9786 (tmm) cc_final: 0.9351 (tmm) REVERT: F 162 ASP cc_start: 0.8647 (t70) cc_final: 0.8381 (t0) outliers start: 40 outliers final: 33 residues processed: 131 average time/residue: 0.1572 time to fit residues: 36.1183 Evaluate side-chains 131 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 B residue 215 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 470 LEU 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 989 LEU 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 1208 MET Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain F residue 177 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 19 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 175 optimal weight: 40.0000 chunk 166 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031895 restraints weight = 173285.968| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 4.74 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 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 = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27552 Z= 0.147 Angle : 0.570 9.816 37785 Z= 0.293 Chirality : 0.042 0.246 4321 Planarity : 0.004 0.052 4628 Dihedral : 17.383 176.420 4664 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.41 % Allowed : 14.97 % Favored : 83.62 % 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: 0.65 (0.15), residues: 3212 helix: 1.72 (0.16), residues: 1205 sheet: 0.20 (0.27), residues: 397 loop : -0.49 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 325 TYR 0.023 0.001 TYR C 91 PHE 0.010 0.001 PHE C 153 TRP 0.015 0.001 TRP D 223 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00331 (27544) covalent geometry : angle 0.56595 (37773) hydrogen bonds : bond 0.03730 ( 1161) hydrogen bonds : angle 4.26665 ( 3207) metal coordination : bond 0.00979 ( 8) metal coordination : angle 3.89727 ( 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 137 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9232 (tmm) cc_final: 0.8923 (ppp) REVERT: C 607 MET cc_start: 0.8841 (mtm) cc_final: 0.8514 (mtm) REVERT: D 92 MET cc_start: 0.8797 (mmm) cc_final: 0.7182 (ppp) REVERT: D 143 MET cc_start: 0.8656 (tmm) cc_final: 0.8381 (tmm) REVERT: D 205 MET cc_start: 0.7902 (mmm) cc_final: 0.7642 (mmm) REVERT: D 376 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 418 LEU cc_start: 0.8962 (mt) cc_final: 0.8695 (mp) REVERT: D 581 MET cc_start: 0.8906 (mtp) cc_final: 0.8704 (mtm) REVERT: D 666 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9235 (p) REVERT: D 718 ASP cc_start: 0.9421 (t70) cc_final: 0.9158 (t0) REVERT: D 733 MET cc_start: 0.8835 (tmm) cc_final: 0.8276 (tmm) REVERT: D 983 MET cc_start: 0.8933 (mmm) cc_final: 0.8595 (mmm) REVERT: D 1112 MET cc_start: 0.8197 (tpt) cc_final: 0.7238 (tpt) REVERT: F 147 MET cc_start: 0.9790 (tmm) cc_final: 0.9384 (tmm) REVERT: F 162 ASP cc_start: 0.8629 (t70) cc_final: 0.8362 (t0) outliers start: 37 outliers final: 34 residues processed: 134 average time/residue: 0.1568 time to fit residues: 36.8368 Evaluate side-chains 134 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 424 VAL Chi-restraints excluded: chain C residue 470 LEU 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 989 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 220 GLU 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 E residue 67 TYR 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: 10.0000 chunk 287 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 203 optimal weight: 0.6980 chunk 262 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN F 137 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.045583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.030725 restraints weight = 177173.563| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 4.71 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27552 Z= 0.277 Angle : 0.665 12.083 37785 Z= 0.342 Chirality : 0.044 0.249 4321 Planarity : 0.004 0.052 4628 Dihedral : 17.486 176.922 4664 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.56 % Allowed : 15.20 % Favored : 83.24 % 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: 0.42 (0.15), residues: 3212 helix: 1.52 (0.15), residues: 1212 sheet: 0.02 (0.27), residues: 407 loop : -0.60 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 325 TYR 0.021 0.001 TYR C 91 PHE 0.016 0.001 PHE F 121 TRP 0.016 0.001 TRP D 723 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00616 (27544) covalent geometry : angle 0.66005 (37773) hydrogen bonds : bond 0.04614 ( 1161) hydrogen bonds : angle 4.55282 ( 3207) metal coordination : bond 0.01738 ( 8) metal coordination : angle 4.58706 ( 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 138 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9101 (tmm) cc_final: 0.8746 (tmm) REVERT: C 607 MET cc_start: 0.8790 (mtm) cc_final: 0.8538 (mtm) REVERT: D 92 MET cc_start: 0.8871 (mmm) cc_final: 0.7262 (ppp) REVERT: D 143 MET cc_start: 0.8710 (tmm) cc_final: 0.8441 (tmm) REVERT: D 205 MET cc_start: 0.7911 (mmm) cc_final: 0.7652 (mmm) REVERT: D 376 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 666 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9224 (p) REVERT: D 733 MET cc_start: 0.8882 (tmm) cc_final: 0.8365 (tmm) REVERT: D 749 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7201 (t80) REVERT: D 983 MET cc_start: 0.9036 (mmm) cc_final: 0.8609 (mmm) REVERT: F 147 MET cc_start: 0.9794 (tmm) cc_final: 0.9361 (tmm) REVERT: F 162 ASP cc_start: 0.8628 (t70) cc_final: 0.8295 (t0) outliers start: 41 outliers final: 32 residues processed: 134 average time/residue: 0.1569 time to fit residues: 36.9497 Evaluate side-chains 129 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 B residue 215 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 470 LEU 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 989 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 220 GLU 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 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 749 TYR 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 E residue 67 TYR 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: 0.3980 chunk 279 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** 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 = 0.3262 r_free = 0.3262 target = 0.046529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.031713 restraints weight = 172433.194| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 4.71 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 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 = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27552 Z= 0.139 Angle : 0.584 10.422 37785 Z= 0.301 Chirality : 0.042 0.243 4321 Planarity : 0.004 0.053 4628 Dihedral : 17.440 176.682 4664 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.41 % Allowed : 15.39 % Favored : 83.21 % 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: 1.65 (0.16), residues: 1205 sheet: 0.18 (0.28), residues: 392 loop : -0.55 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 97 TYR 0.023 0.001 TYR C 91 PHE 0.010 0.001 PHE C 153 TRP 0.010 0.001 TRP C 938 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00313 (27544) covalent geometry : angle 0.57980 (37773) hydrogen bonds : bond 0.03797 ( 1161) hydrogen bonds : angle 4.30819 ( 3207) metal coordination : bond 0.00932 ( 8) metal coordination : angle 4.15619 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4636.65 seconds wall clock time: 80 minutes 50.01 seconds (4850.01 seconds total)