Starting phenix.real_space_refine on Mon Sep 14 02:17:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckq_30390/09_2026/7ckq_30390.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 87 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 17082 2.51 5 N 4741 2.21 5 O 5505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27484 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1540 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1538 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 7446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 7446 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1010} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 972 Unresolved non-hydrogen angles: 1203 Unresolved non-hydrogen dihedrals: 824 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'TYR:plan': 16, 'ARG:plan': 46, 'GLU:plan': 24, 'PHE:plan': 12, 'ASP:plan': 19, 'ASN:plan1': 9, 'GLN:plan1': 6, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 615 Chain: "D" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 7854 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 234} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1085} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1126 Unresolved non-hydrogen angles: 1403 Unresolved non-hydrogen dihedrals: 926 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'TYR:plan': 8, 'TRP:plan': 2, 'GLU:plan': 40, 'HIS:plan': 10, 'ARG:plan': 38, 'ASP:plan': 15, 'PHE:plan': 7, 'GLN:plan1': 17, 'ASN:plan1': 14} Unresolved non-hydrogen planarities: 638 Chain: "E" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 405 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2030 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 3, 'GLU:plan': 10, 'TYR:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 126 Chain: "1" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1028 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 756 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2187 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 263} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2184 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 263} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "H" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 463 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 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} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P4P': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P4P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10941 SG CYS D 60 105.868 67.722 81.401 1.00 70.25 S ATOM 11048 SG CYS D 75 110.409 69.092 81.578 1.00 82.89 S ATOM 16179 SG CYS D 818 75.584 77.686 137.816 1.00 90.51 S ATOM 16628 SG CYS D 892 74.676 78.775 134.318 1.00 83.99 S ATOM 16671 SG CYS D 899 76.071 74.909 135.470 1.00 86.21 S ATOM 16687 SG CYS D 902 72.139 76.497 136.997 1.00 90.25 S Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 27484 At special positions: 0 Unit cell: (150, 139, 168, 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 66 16.00 P 87 15.00 Mg 1 11.99 O 5505 8.00 N 4741 7.00 C 17082 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 75 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 902 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 892 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 899 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 818 " Number of angles added : 6 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6688 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 41 sheets defined 36.8% alpha, 10.1% beta 31 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.676A pdb=" N ARG A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 205 through 221 removed outlier: 4.099A pdb=" N ILE A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.591A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.730A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.594A pdb=" N ASP C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.574A pdb=" N GLU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.608A pdb=" N ALA C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.920A pdb=" N LEU C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 288 removed outlier: 4.021A pdb=" N PHE C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 287 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 394 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.667A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 449' Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.639A pdb=" N PHE C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.544A pdb=" N LYS C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 499 removed outlier: 3.916A pdb=" N ALA C 499 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.767A pdb=" N ARG C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 500 through 505' Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.752A pdb=" N TYR C 511 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.636A pdb=" N GLN C 617 " --> pdb=" O SER C 614 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 619 " --> pdb=" O LYS C 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 619' Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.896A pdb=" N MET C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 855 through 861 Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 967 through 983 removed outlier: 4.160A pdb=" N VAL C 971 " --> pdb=" O ASN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1004 through 1009 Processing helix chain 'C' and resid 1076 through 1087 removed outlier: 3.724A pdb=" N TYR C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C1087 " --> pdb=" O LEU C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1097 removed outlier: 3.943A pdb=" N LEU C1092 " --> pdb=" O ALA C1088 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C1097 " --> pdb=" O GLN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1113 Processing helix chain 'C' and resid 1125 through 1138 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.762A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.696A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.048A pdb=" N GLU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 253 through 273 removed outlier: 4.124A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 removed outlier: 3.520A pdb=" N VAL D 281 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 removed outlier: 4.563A pdb=" N ARG D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 302' Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.842A pdb=" N GLU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 378 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.887A pdb=" N ALA D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 4.486A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.990A pdb=" N GLY D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 527 Processing helix chain 'D' and resid 561 through 568 removed outlier: 3.522A pdb=" N LEU D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 632 removed outlier: 3.928A pdb=" N HIS D 632 " --> pdb=" O PHE D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 655 removed outlier: 3.824A pdb=" N LYS D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 689 removed outlier: 4.094A pdb=" N GLN D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU D 671 " --> pdb=" O ASP D 667 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 718 removed outlier: 4.096A pdb=" N ILE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 removed outlier: 3.585A pdb=" N SER D 732 " --> pdb=" O MET D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 746 removed outlier: 3.596A pdb=" N PHE D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 744 " --> pdb=" O ASN D 740 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 745 " --> pdb=" O PHE D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 808 removed outlier: 3.807A pdb=" N HIS D 781 " --> pdb=" O PHE D 777 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 875 Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 919 through 928 Processing helix chain 'D' and resid 929 through 933 removed outlier: 3.663A pdb=" N THR D 932 " --> pdb=" O GLU D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 953 through 961 Processing helix chain 'D' and resid 1039 through 1051 removed outlier: 3.656A pdb=" N VAL D1043 " --> pdb=" O ASP D1039 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D1051 " --> pdb=" O LEU D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1059 removed outlier: 4.289A pdb=" N TYR D1055 " --> pdb=" O VAL D1051 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D1056 " --> pdb=" O GLN D1052 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET D1057 " --> pdb=" O LYS D1053 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D1058 " --> pdb=" O VAL D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1066 removed outlier: 4.076A pdb=" N HIS D1066 " --> pdb=" O GLY D1063 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1063 through 1066' Processing helix chain 'D' and resid 1067 through 1073 removed outlier: 4.127A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1076 No H-bonds generated for 'chain 'D' and resid 1074 through 1076' Processing helix chain 'D' and resid 1093 through 1102 Processing helix chain 'D' and resid 1141 through 1153 Processing helix chain 'D' and resid 1162 through 1168 removed outlier: 3.899A pdb=" N ILE D1166 " --> pdb=" O LYS D1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.664A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR E 21 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.568A pdb=" N LYS E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 116 through 130 removed outlier: 3.624A pdb=" N GLU F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 150 removed outlier: 3.994A pdb=" N GLU F 140 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 185 through 204 removed outlier: 4.057A pdb=" N TYR F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 234 removed outlier: 3.883A pdb=" N THR F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 243 removed outlier: 4.160A pdb=" N ALA F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.732A pdb=" N LYS F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN F 261 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 4.079A pdb=" N ASP F 280 " --> pdb=" O HIS F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 314 through 323 removed outlier: 4.532A pdb=" N PHE F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 342 through 359 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'G' and resid 7 through 14 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 54 through 63 Processing helix chain 'G' and resid 65 through 73 removed outlier: 3.638A pdb=" N MET G 69 " --> pdb=" O PRO G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 115 Processing helix chain 'G' and resid 148 through 163 removed outlier: 3.586A pdb=" N TYR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE G 159 " --> pdb=" O LEU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 244 removed outlier: 3.632A pdb=" N LEU G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 15 Processing helix chain 'I' and resid 18 through 29 Processing helix chain 'I' and resid 49 through 53 removed outlier: 3.505A pdb=" N HIS I 52 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 63 Processing helix chain 'I' and resid 65 through 73 removed outlier: 3.868A pdb=" N MET I 69 " --> pdb=" O PRO I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 115 Processing helix chain 'I' and resid 148 through 151 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 225 through 244 removed outlier: 3.500A pdb=" N TYR I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE I 230 " --> pdb=" O PRO I 226 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.520A pdb=" N VAL H 33 " --> pdb=" O SER H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.772A pdb=" N TYR H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28 removed outlier: 7.139A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 175 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.854A pdb=" N LYS A 95 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 142 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 52 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 145 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.831A pdb=" N GLU A 98 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 101 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 136 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.530A pdb=" N GLY A 105 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.524A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN B 179 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 88 removed outlier: 4.590A pdb=" N LYS B 88 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 119 " --> pdb=" O LYS B 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.505A pdb=" N LEU B 130 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.925A pdb=" N THR B 149 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 15 through 16 removed outlier: 6.494A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 62 through 71 removed outlier: 3.762A pdb=" N ILE C 67 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS C 95 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR C 69 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG C 93 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 410 removed outlier: 3.917A pdb=" N SER C 530 " --> pdb=" O CYS C 515 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.783A pdb=" N SER C 147 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 190 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 536 through 537 removed outlier: 3.638A pdb=" N ASP C 562 " --> pdb=" O TYR C 547 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537 removed outlier: 3.752A pdb=" N VAL C 574 " --> pdb=" O ARG C 595 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 592 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 603 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 601 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 682 through 685 removed outlier: 3.554A pdb=" N VAL C 692 " --> pdb=" O ASP C 708 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AC3, first strand: chain 'C' and resid 955 through 957 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 800 removed outlier: 7.534A pdb=" N SER C 789 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS C 916 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N HIS C 791 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL C 914 " --> pdb=" O HIS C 791 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU C 793 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR C 912 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 795 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG C 910 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 797 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 908 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA C 799 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU C 908 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL C 892 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG C 910 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 890 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR C 912 " --> pdb=" O HIS C 888 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 885 " --> pdb=" O VAL C 836 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 808 through 809 removed outlier: 3.529A pdb=" N GLU C 808 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 924 through 926 Processing sheet with id=AC7, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.906A pdb=" N GLY D 340 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D 342 " --> pdb=" O MET D 455 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET D 455 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 426 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN D 424 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AC9, first strand: chain 'D' and resid 34 through 35 removed outlier: 7.252A pdb=" N ILE D 34 " --> pdb=" O ARG F 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 94 through 101 removed outlier: 10.646A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.568A pdb=" N VAL D 135 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 169 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN D 167 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 242 through 243 removed outlier: 7.081A pdb=" N PHE D 249 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 344 through 346 Processing sheet with id=AD5, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.504A pdb=" N LEU D 357 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AD7, first strand: chain 'D' and resid 979 through 980 Processing sheet with id=AD8, first strand: chain 'G' and resid 35 through 36 removed outlier: 3.810A pdb=" N TYR G 44 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.548A pdb=" N TYR G 217 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG G 216 " --> pdb=" O ILE G 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 209 through 211 removed outlier: 3.808A pdb=" N ILE G 135 " --> pdb=" O THR G 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE G 190 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA G 172 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE G 174 " --> pdb=" O VAL G 251 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL G 251 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 273 " --> pdb=" O TYR G 252 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL G 270 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR G 222 " --> pdb=" O VAL G 270 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.787A pdb=" N TYR I 44 " --> pdb=" O TYR I 35 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.662A pdb=" N ARG I 216 " --> pdb=" O ILE I 276 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 209 through 211 removed outlier: 3.734A pdb=" N ILE I 135 " --> pdb=" O THR I 192 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE I 190 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS I 189 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA I 172 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE I 174 " --> pdb=" O VAL I 251 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL I 251 " --> pdb=" O PHE I 174 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS I 273 " --> pdb=" O TYR I 252 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 256 " --> pdb=" O ARG I 269 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL I 270 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR I 222 " --> pdb=" O VAL I 270 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 21 through 26 removed outlier: 7.097A pdb=" N LYS H 4 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE H 47 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE H 6 " --> pdb=" O GLU H 45 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2679 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9134 1.35 - 1.48: 6664 1.48 - 1.61: 12110 1.61 - 1.74: 63 1.74 - 1.87: 124 Bond restraints: 28095 Sorted by residual: bond pdb=" C1' DC 2 30 " pdb=" N1 DC 2 30 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" C ASP C 551 " pdb=" N PRO C 552 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.20e-02 6.94e+03 1.57e+01 bond pdb=" C3' DC 1 76 " pdb=" O3' DC 1 76 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" C1C P4P G 300 " pdb=" P P4P G 300 " ideal model delta sigma weight residual 1.795 1.867 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1A P4P G 300 " pdb=" P P4P G 300 " ideal model delta sigma weight residual 1.795 1.866 -0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 28090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 37742 2.11 - 4.22: 759 4.22 - 6.33: 83 6.33 - 8.44: 33 8.44 - 10.54: 8 Bond angle restraints: 38625 Sorted by residual: angle pdb=" N GLU D 834 " pdb=" CA GLU D 834 " pdb=" C GLU D 834 " ideal model delta sigma weight residual 109.52 120.06 -10.54 1.55e+00 4.16e-01 4.63e+01 angle pdb=" N ILE D 836 " pdb=" CA ILE D 836 " pdb=" C ILE D 836 " ideal model delta sigma weight residual 109.58 116.61 -7.03 1.29e+00 6.01e-01 2.97e+01 angle pdb=" N3 DT 2 31 " pdb=" C4 DT 2 31 " pdb=" O4 DT 2 31 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT 1 47 " pdb=" C4 DT 1 47 " pdb=" O4 DT 1 47 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" C3' DC 1 76 " pdb=" O3' DC 1 76 " pdb=" P DT 1 77 " ideal model delta sigma weight residual 119.70 124.99 -5.29 1.20e+00 6.94e-01 1.94e+01 ... (remaining 38620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 16218 35.53 - 71.06: 491 71.06 - 106.59: 25 106.59 - 142.12: 4 142.12 - 177.65: 2 Dihedral angle restraints: 16740 sinusoidal: 6379 harmonic: 10361 Sorted by residual: dihedral pdb=" CA PRO H 49 " pdb=" C PRO H 49 " pdb=" N VAL H 50 " pdb=" CA VAL H 50 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LYS C 702 " pdb=" C LYS C 702 " pdb=" N VAL C 703 " pdb=" CA VAL C 703 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA GLY C 866 " pdb=" C GLY C 866 " pdb=" N GLU C 867 " pdb=" CA GLU C 867 " ideal model delta harmonic sigma weight residual 180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 16737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3983 0.075 - 0.150: 556 0.150 - 0.225: 42 0.225 - 0.301: 6 0.301 - 0.376: 1 Chirality restraints: 4588 Sorted by residual: chirality pdb=" CB ILE I 255 " pdb=" CA ILE I 255 " pdb=" CG1 ILE I 255 " pdb=" CG2 ILE I 255 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE G 255 " pdb=" CA ILE G 255 " pdb=" CG1 ILE G 255 " pdb=" CG2 ILE G 255 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB THR D 142 " pdb=" CA THR D 142 " pdb=" OG1 THR D 142 " pdb=" CG2 THR D 142 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4585 not shown) Planarity restraints: 4763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 234 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO D 235 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 988 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C GLN D 988 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN D 988 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN D 989 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 475 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO C 476 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 476 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 476 " 0.033 5.00e-02 4.00e+02 ... (remaining 4760 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 845 2.70 - 3.25: 24442 3.25 - 3.80: 43845 3.80 - 4.35: 53226 4.35 - 4.90: 86554 Nonbonded interactions: 208912 Sorted by model distance: nonbonded pdb=" O GLN A 179 " pdb=" OG1 THR A 195 " model vdw 2.153 3.040 nonbonded pdb=" OD2 ASP D 451 " pdb="MG MG D1501 " model vdw 2.181 2.170 nonbonded pdb=" OG SER I 181 " pdb=" OE1 GLU I 184 " model vdw 2.298 3.040 nonbonded pdb=" O ARG B 42 " pdb=" OG SER B 46 " model vdw 2.326 3.040 nonbonded pdb=" O ILE G 134 " pdb=" OG1 THR G 210 " model vdw 2.333 3.040 ... (remaining 208907 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 6 through 15 or (resid 16 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 40 or (resid 41 through \ 42 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE or name CZ )) or resid 43 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 67 or (resid 68 and (na \ me N or name CA or name C or name O or name CB )) or resid 69 through 97 or (res \ id 98 and (name N or name CA or name C or name O or name CB )) or resid 99 or (r \ esid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 o \ r (resid 102 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 03 through 131 or (resid 132 and (name N or name CA or name C or name O or name \ CB )) or resid 133 through 162 or (resid 163 and (name N or name CA or name C or \ name O or name CB )) or resid 164 through 200 or (resid 201 and (name N or name \ CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 and \ (name N or name CA or name C or name O or name CB )) or resid 208 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 213 through 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 225)) selection = (chain 'B' and (resid 6 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or (resid 11 and (name N or name CA or name C or name O \ or name CB or name OG1)) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 16 or (resid 17 throug \ h 19 and (name N or name CA or name C or name O or name CB )) or resid 20 throug \ h 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or re \ sid 24 through 29 or (resid 30 and (name N or name CA or name C or name O or nam \ e CB )) or resid 31 through 33 or (resid 34 and (name N or name CA or name C or \ name O or name CB or name OG1)) or resid 35 through 47 or (resid 48 and (name N \ or name CA or name C or name O or name CB )) or resid 49 through 75 or (resid 76 \ through 77 and (name N or name CA or name C or name O or name CB or name OG1)) \ or resid 78 or (resid 79 and (name N or name CA or name C or name O or name CB o \ r name CG1)) or resid 80 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 107 through 121 or (resid 122 an \ d (name N or name CA or name C or name O or name CB )) or resid 123 or (resid 12 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 128 or (resid 129 and (name N or name CA or name C or name O or name CB or name \ OG1)) or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB or name OG1)) or resid 142 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or resid 149 through 165 or (resid 166 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 16 \ 7 through 170 or (resid 171 and (name N or name CA or name C or name O or name C \ B or name OG1)) or resid 172 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 183 or (resid 184 and (name \ N or name CA or name C or name O or name CB )) or resid 185 through 190 or (res \ id 191 and (name N or name CA or name C or name O or name CB )) or resid 192 thr \ ough 225)) } ncs_group { reference = (chain 'G' and (resid 2 through 11 or (resid 12 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 38 or (resid 39 and (nam \ e N or name CA or name C or name O or name CB )) or resid 40 through 46 or (resi \ d 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throug \ h 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or re \ sid 51 through 144 or (resid 145 and (name N or name CA or name C or name O or n \ ame CB )) or resid 146 through 266 or (resid 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 through 271 or (resid 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 through 300)) selection = (chain 'I' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 9 or (resid 10 and (name N o \ r name CA or name C or name O or name CB )) or resid 11 through 146 or (resid 14 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 148 through \ 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) or re \ sid 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) o \ r resid 158 through 275 or (resid 276 through 277 and (name N or name CA or name \ C or name O or name CB )) or resid 300)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.120 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 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 : 0.006 0.439 28101 Z= 0.302 Angle : 0.742 21.928 38631 Z= 0.438 Chirality : 0.050 0.376 4588 Planarity : 0.005 0.068 4763 Dihedral : 15.908 177.650 10052 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.38 % Rotamer: Outliers : 0.30 % Allowed : 7.43 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.73 (0.10), residues: 3558 helix: -3.47 (0.08), residues: 1251 sheet: -1.92 (0.27), residues: 309 loop : -3.22 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.018 0.001 TYR I 268 PHE 0.017 0.001 PHE I 230 TRP 0.004 0.001 TRP C 169 HIS 0.006 0.000 HIS D 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.25 (28095) covalent geometry : angle 0.71291 / 0.44 (38625) hydrogen bonds : bond 0.19691 / 13.46 ( 1020) hydrogen bonds : angle 8.13376 / 5.54 ( 2839) metal coordination : bond 0.33615 / 17.10 ( 6) metal coordination : angle 16.39672 / 9.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 799 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7989 (tp) cc_final: 0.7677 (tp) REVERT: A 167 ASP cc_start: 0.8157 (m-30) cc_final: 0.7034 (p0) REVERT: B 82 ILE cc_start: 0.8053 (mt) cc_final: 0.7841 (tp) REVERT: B 216 ILE cc_start: 0.9406 (mm) cc_final: 0.9178 (mm) REVERT: C 127 ILE cc_start: 0.9250 (mp) cc_final: 0.8822 (mt) REVERT: C 471 MET cc_start: 0.5482 (tmm) cc_final: 0.5160 (tmm) REVERT: C 479 GLU cc_start: 0.8825 (tt0) cc_final: 0.8297 (tt0) REVERT: C 489 LEU cc_start: 0.6599 (mp) cc_final: 0.4822 (mt) REVERT: C 646 GLN cc_start: 0.7911 (tp40) cc_final: 0.7660 (tp40) REVERT: C 772 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 935 ILE cc_start: 0.9122 (mm) cc_final: 0.8869 (mm) REVERT: C 946 TYR cc_start: 0.7399 (p90) cc_final: 0.7042 (p90) REVERT: C 1079 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6912 (mt-10) REVERT: D 234 ILE cc_start: 0.9260 (tp) cc_final: 0.8991 (tp) REVERT: D 290 GLU cc_start: 0.8405 (pt0) cc_final: 0.8162 (pt0) REVERT: D 365 LEU cc_start: 0.8314 (mm) cc_final: 0.6377 (mm) REVERT: D 800 LEU cc_start: 0.6909 (tp) cc_final: 0.6641 (tt) REVERT: D 861 LEU cc_start: 0.7927 (pt) cc_final: 0.7610 (mp) REVERT: D 1161 LEU cc_start: 0.5833 (pt) cc_final: 0.5538 (pt) REVERT: F 208 THR cc_start: 0.9082 (p) cc_final: 0.8730 (p) REVERT: F 214 HIS cc_start: 0.6523 (m-70) cc_final: 0.6246 (m-70) REVERT: F 238 THR cc_start: 0.7267 (m) cc_final: 0.6797 (m) REVERT: F 242 ILE cc_start: 0.8963 (mt) cc_final: 0.8719 (tp) REVERT: F 252 LYS cc_start: 0.9299 (tppt) cc_final: 0.9035 (tptp) REVERT: F 352 LYS cc_start: 0.8120 (mttp) cc_final: 0.7379 (tppt) REVERT: G 191 PHE cc_start: 0.7677 (p90) cc_final: 0.7435 (p90) REVERT: I 160 GLU cc_start: 0.8375 (pp20) cc_final: 0.8081 (pp20) REVERT: I 185 MET cc_start: 0.3410 (ptm) cc_final: 0.1158 (tmm) REVERT: H 3 TYR cc_start: 0.5545 (m-80) cc_final: 0.5077 (m-10) REVERT: H 6 PHE cc_start: 0.7974 (m-80) cc_final: 0.7702 (m-10) REVERT: H 15 PRO cc_start: 0.6685 (Cg_endo) cc_final: 0.5858 (Cg_exo) REVERT: H 33 VAL cc_start: 0.9372 (t) cc_final: 0.9081 (p) REVERT: H 48 THR cc_start: 0.5094 (p) cc_final: 0.4802 (p) outliers start: 7 outliers final: 2 residues processed: 804 average time/residue: 0.1985 time to fit residues: 246.4689 Evaluate side-chains 518 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 516 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN B 63 HIS B 190 ASN C 38 GLN C 100 ASN C 419 GLN C 475 ASN C 578 ASN C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 GLN D1058 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN F 277 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN G 149 ASN I 167 ASN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 ASN I 199 GLN I 259 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.132890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.116178 restraints weight = 104192.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118687 restraints weight = 68537.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.120457 restraints weight = 48695.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.121745 restraints weight = 37011.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.122673 restraints weight = 29659.343| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28101 Z= 0.144 Angle : 0.625 13.672 38631 Z= 0.330 Chirality : 0.044 0.243 4588 Planarity : 0.005 0.086 4763 Dihedral : 15.527 179.225 4753 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.38 (0.12), residues: 3558 helix: -1.71 (0.12), residues: 1269 sheet: -1.73 (0.27), residues: 340 loop : -2.80 (0.12), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 259 TYR 0.023 0.001 TYR I 25 PHE 0.021 0.002 PHE D 631 TRP 0.008 0.001 TRP C 766 HIS 0.010 0.001 HIS D 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (28095) covalent geometry : angle 0.62448 / 0.33 (38625) hydrogen bonds : bond 0.03958 / 2.80 ( 1020) hydrogen bonds : angle 5.71391 / 3.95 ( 2839) metal coordination : bond 0.00901 / 0.48 ( 6) metal coordination : angle 1.68767 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 618 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8196 (tp) cc_final: 0.7720 (tp) REVERT: A 67 THR cc_start: 0.6681 (p) cc_final: 0.6419 (p) REVERT: A 167 ASP cc_start: 0.8409 (m-30) cc_final: 0.7946 (p0) REVERT: C 127 ILE cc_start: 0.9246 (mp) cc_final: 0.8901 (mt) REVERT: C 479 GLU cc_start: 0.8974 (tt0) cc_final: 0.8343 (mm-30) REVERT: C 489 LEU cc_start: 0.6106 (mp) cc_final: 0.5794 (mp) REVERT: C 764 MET cc_start: 0.9141 (ppp) cc_final: 0.8465 (ppp) REVERT: C 772 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 806 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7274 (Cg_exo) REVERT: C 841 LEU cc_start: 0.7950 (mm) cc_final: 0.7260 (mm) REVERT: C 1037 MET cc_start: 0.6840 (mmp) cc_final: 0.6614 (mmp) REVERT: C 1079 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7147 (mt-10) REVERT: C 1113 ILE cc_start: 0.7534 (pt) cc_final: 0.7332 (pt) REVERT: C 1135 LEU cc_start: 0.8756 (mt) cc_final: 0.8504 (mt) REVERT: D 51 ILE cc_start: 0.7819 (mt) cc_final: 0.7592 (mt) REVERT: D 81 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7506 (tm-30) REVERT: D 120 MET cc_start: 0.4205 (pmm) cc_final: 0.3494 (pmm) REVERT: D 239 ARG cc_start: 0.9199 (ptt-90) cc_final: 0.8972 (ptt-90) REVERT: D 290 GLU cc_start: 0.8653 (pt0) cc_final: 0.8368 (pt0) REVERT: D 861 LEU cc_start: 0.8278 (pt) cc_final: 0.7782 (mt) REVERT: D 1143 THR cc_start: 0.8579 (m) cc_final: 0.8044 (t) REVERT: D 1161 LEU cc_start: 0.6430 (pt) cc_final: 0.6141 (pt) REVERT: F 161 LEU cc_start: 0.8595 (tp) cc_final: 0.8175 (tp) REVERT: F 214 HIS cc_start: 0.6957 (m-70) cc_final: 0.6420 (m-70) REVERT: F 246 MET cc_start: 0.5211 (mmm) cc_final: 0.4949 (mmm) REVERT: F 252 LYS cc_start: 0.9500 (tppt) cc_final: 0.9128 (tptp) REVERT: F 352 LYS cc_start: 0.8264 (mttp) cc_final: 0.7704 (tppt) REVERT: G 98 LEU cc_start: 0.8761 (mt) cc_final: 0.8502 (tt) REVERT: G 148 LEU cc_start: 0.8786 (pp) cc_final: 0.8545 (pp) REVERT: I 16 ASN cc_start: 0.8408 (m110) cc_final: 0.8049 (m110) REVERT: I 91 ILE cc_start: 0.9034 (tt) cc_final: 0.8780 (tt) REVERT: I 185 MET cc_start: 0.3693 (ptm) cc_final: 0.1289 (ppp) REVERT: I 207 MET cc_start: 0.5536 (mmp) cc_final: 0.5271 (mmm) REVERT: H 5 VAL cc_start: 0.8517 (t) cc_final: 0.7942 (t) REVERT: H 19 LYS cc_start: 0.8036 (ptpt) cc_final: 0.7791 (ptpt) REVERT: H 33 VAL cc_start: 0.9575 (t) cc_final: 0.9278 (p) REVERT: H 39 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.4385 (pm20) outliers start: 3 outliers final: 2 residues processed: 620 average time/residue: 0.1760 time to fit residues: 176.4475 Evaluate side-chains 468 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 465 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 353 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 301 optimal weight: 30.0000 chunk 337 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 156 optimal weight: 0.0070 chunk 117 optimal weight: 8.9990 chunk 341 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 HIS B 143 GLN C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN C 720 GLN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN F 142 ASN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 177 GLN I 189 HIS I 197 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.130386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.113751 restraints weight = 104507.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.116187 restraints weight = 69860.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.117965 restraints weight = 50224.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.119257 restraints weight = 38337.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.120205 restraints weight = 30864.332| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 28101 Z= 0.134 Angle : 0.594 11.547 38631 Z= 0.315 Chirality : 0.044 0.266 4588 Planarity : 0.005 0.143 4763 Dihedral : 15.483 178.629 4753 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.13), residues: 3558 helix: -0.98 (0.14), residues: 1268 sheet: -1.49 (0.26), residues: 380 loop : -2.55 (0.12), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG G 269 TYR 0.029 0.001 TYR I 179 PHE 0.034 0.002 PHE H 6 TRP 0.007 0.001 TRP C 169 HIS 0.011 0.001 HIS C 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (28095) covalent geometry : angle 0.59433 / 0.31 (38625) hydrogen bonds : bond 0.03553 / 2.48 ( 1020) hydrogen bonds : angle 5.31757 / 3.70 ( 2839) metal coordination : bond 0.00096 / 0.05 ( 6) metal coordination : angle 1.09502 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 585 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8366 (m-30) cc_final: 0.8011 (p0) REVERT: B 143 GLN cc_start: 0.6894 (tm130) cc_final: 0.6649 (tm-30) REVERT: C 73 GLU cc_start: 0.7540 (pm20) cc_final: 0.7280 (pm20) REVERT: C 127 ILE cc_start: 0.9242 (mp) cc_final: 0.8828 (mt) REVERT: C 479 GLU cc_start: 0.8796 (tt0) cc_final: 0.8257 (mm-30) REVERT: C 489 LEU cc_start: 0.6264 (mp) cc_final: 0.5833 (mp) REVERT: C 639 MET cc_start: 0.8156 (tpp) cc_final: 0.7920 (tpp) REVERT: C 662 MET cc_start: 0.6736 (ppp) cc_final: 0.6318 (ppp) REVERT: C 764 MET cc_start: 0.9273 (ppp) cc_final: 0.8053 (ppp) REVERT: C 772 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 966 MET cc_start: 0.8219 (ptp) cc_final: 0.7988 (ptp) REVERT: C 1073 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 1079 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7209 (mt-10) REVERT: C 1113 ILE cc_start: 0.7698 (pt) cc_final: 0.7459 (pt) REVERT: C 1135 LEU cc_start: 0.8848 (mt) cc_final: 0.8399 (mt) REVERT: D 18 ASP cc_start: 0.8287 (m-30) cc_final: 0.7311 (p0) REVERT: D 290 GLU cc_start: 0.8595 (pt0) cc_final: 0.8308 (pt0) REVERT: D 587 GLU cc_start: 0.5157 (tp30) cc_final: 0.4623 (tp30) REVERT: D 753 ASN cc_start: 0.7985 (m110) cc_final: 0.7761 (m110) REVERT: D 759 ILE cc_start: 0.7384 (mt) cc_final: 0.7116 (mt) REVERT: D 861 LEU cc_start: 0.8289 (pt) cc_final: 0.7785 (mt) REVERT: F 158 MET cc_start: 0.6466 (pmm) cc_final: 0.5931 (pmm) REVERT: F 161 LEU cc_start: 0.8736 (tp) cc_final: 0.8282 (tp) REVERT: F 214 HIS cc_start: 0.6907 (m-70) cc_final: 0.6385 (m-70) REVERT: F 238 THR cc_start: 0.7623 (m) cc_final: 0.7417 (m) REVERT: F 246 MET cc_start: 0.5414 (mmm) cc_final: 0.5101 (mmm) REVERT: F 252 LYS cc_start: 0.9480 (tppt) cc_final: 0.9128 (tptp) REVERT: F 344 GLU cc_start: 0.7099 (tp30) cc_final: 0.6828 (mt-10) REVERT: G 148 LEU cc_start: 0.8763 (pp) cc_final: 0.8527 (pp) REVERT: I 16 ASN cc_start: 0.8420 (m110) cc_final: 0.8046 (m110) REVERT: I 60 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7568 (tptt) REVERT: I 92 ARG cc_start: 0.8672 (tpt170) cc_final: 0.8122 (mmm-85) REVERT: I 133 ARG cc_start: 0.6678 (mtp180) cc_final: 0.6162 (mtp180) REVERT: I 185 MET cc_start: 0.3572 (ptm) cc_final: 0.0540 (tmm) REVERT: I 207 MET cc_start: 0.5451 (mmp) cc_final: 0.5041 (mmm) REVERT: H 19 LYS cc_start: 0.7766 (ptpt) cc_final: 0.7453 (ptpt) REVERT: H 33 VAL cc_start: 0.9549 (t) cc_final: 0.9285 (p) outliers start: 5 outliers final: 2 residues processed: 587 average time/residue: 0.1623 time to fit residues: 157.3066 Evaluate side-chains 457 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 203 optimal weight: 0.0060 chunk 111 optimal weight: 7.9990 overall best weight: 2.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 HIS C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1066 HIS F 142 ASN G 73 GLN I 73 GLN I 90 GLN I 232 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.105398 restraints weight = 105160.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.107687 restraints weight = 70128.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.109333 restraints weight = 50625.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.110552 restraints weight = 38984.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.111437 restraints weight = 31595.715| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28101 Z= 0.208 Angle : 0.680 11.784 38631 Z= 0.361 Chirality : 0.045 0.249 4588 Planarity : 0.005 0.072 4763 Dihedral : 15.570 178.294 4753 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.13), residues: 3558 helix: -0.58 (0.14), residues: 1291 sheet: -1.42 (0.26), residues: 363 loop : -2.40 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 269 TYR 0.046 0.002 TYR D 577 PHE 0.040 0.003 PHE F 369 TRP 0.019 0.002 TRP C 39 HIS 0.008 0.002 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (28095) covalent geometry : angle 0.67943 / 0.36 (38625) hydrogen bonds : bond 0.03893 / 2.72 ( 1020) hydrogen bonds : angle 5.14337 / 3.56 ( 2839) metal coordination : bond 0.00461 / 0.23 ( 6) metal coordination : angle 1.93304 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 584 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8484 (m-30) cc_final: 0.7974 (p0) REVERT: B 143 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7018 (tm-30) REVERT: C 73 GLU cc_start: 0.7754 (pm20) cc_final: 0.7527 (pm20) REVERT: C 92 LEU cc_start: 0.8374 (tp) cc_final: 0.7947 (tp) REVERT: C 107 LYS cc_start: 0.7736 (tptm) cc_final: 0.7403 (mmtm) REVERT: C 127 ILE cc_start: 0.9326 (mp) cc_final: 0.8891 (mt) REVERT: C 237 TYR cc_start: 0.6964 (t80) cc_final: 0.6275 (t80) REVERT: C 489 LEU cc_start: 0.6749 (mp) cc_final: 0.6358 (mp) REVERT: C 639 MET cc_start: 0.8212 (tpp) cc_final: 0.7963 (tpp) REVERT: C 719 ASN cc_start: 0.8454 (m-40) cc_final: 0.8138 (m110) REVERT: C 764 MET cc_start: 0.9462 (ppp) cc_final: 0.8172 (ppp) REVERT: C 841 LEU cc_start: 0.9243 (tp) cc_final: 0.8872 (tp) REVERT: C 1012 ASP cc_start: 0.8252 (p0) cc_final: 0.7874 (p0) REVERT: C 1079 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 1084 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6569 (tt0) REVERT: C 1113 ILE cc_start: 0.8009 (pt) cc_final: 0.7763 (pt) REVERT: C 1135 LEU cc_start: 0.9004 (mt) cc_final: 0.8548 (mt) REVERT: D 103 HIS cc_start: 0.7438 (t-90) cc_final: 0.6922 (t-90) REVERT: D 290 GLU cc_start: 0.8532 (pt0) cc_final: 0.8096 (pt0) REVERT: D 516 PHE cc_start: 0.8424 (m-80) cc_final: 0.8178 (m-80) REVERT: D 753 ASN cc_start: 0.7905 (m110) cc_final: 0.7651 (m110) REVERT: D 759 ILE cc_start: 0.7280 (mt) cc_final: 0.7012 (mt) REVERT: D 861 LEU cc_start: 0.8390 (pt) cc_final: 0.7951 (mt) REVERT: D 1077 LYS cc_start: 0.6789 (tptm) cc_final: 0.6432 (tptt) REVERT: D 1143 THR cc_start: 0.8786 (m) cc_final: 0.8320 (t) REVERT: D 1161 LEU cc_start: 0.6488 (pt) cc_final: 0.5710 (pt) REVERT: F 158 MET cc_start: 0.7110 (pmm) cc_final: 0.6549 (pmm) REVERT: F 159 LEU cc_start: 0.8601 (tp) cc_final: 0.8310 (tp) REVERT: F 166 GLU cc_start: 0.8890 (mp0) cc_final: 0.8353 (mm-30) REVERT: F 214 HIS cc_start: 0.7130 (m-70) cc_final: 0.6775 (m-70) REVERT: F 246 MET cc_start: 0.6070 (mmm) cc_final: 0.5791 (mmm) REVERT: F 252 LYS cc_start: 0.9536 (tppt) cc_final: 0.9119 (mmmm) REVERT: F 344 GLU cc_start: 0.7429 (tp30) cc_final: 0.6954 (tp30) REVERT: G 57 LYS cc_start: 0.8740 (tptp) cc_final: 0.8442 (tptp) REVERT: G 191 PHE cc_start: 0.8150 (p90) cc_final: 0.7813 (p90) REVERT: G 268 TYR cc_start: 0.7324 (p90) cc_final: 0.6415 (p90) REVERT: I 16 ASN cc_start: 0.8468 (m110) cc_final: 0.8093 (m110) REVERT: I 191 PHE cc_start: 0.5192 (p90) cc_final: 0.4829 (p90) REVERT: I 207 MET cc_start: 0.5616 (mmp) cc_final: 0.4947 (mmm) REVERT: H 6 PHE cc_start: 0.8538 (m-10) cc_final: 0.8234 (m-10) REVERT: H 19 LYS cc_start: 0.7700 (ptpt) cc_final: 0.7326 (ptpt) REVERT: H 33 VAL cc_start: 0.9569 (t) cc_final: 0.9310 (p) outliers start: 5 outliers final: 2 residues processed: 588 average time/residue: 0.1672 time to fit residues: 159.7255 Evaluate side-chains 433 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 431 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 263 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN C 446 GLN C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN ** C 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.116388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099203 restraints weight = 104004.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101505 restraints weight = 67912.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.103197 restraints weight = 48366.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104399 restraints weight = 36864.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.105301 restraints weight = 29685.119| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.190 28101 Z= 0.272 Angle : 0.760 12.833 38631 Z= 0.399 Chirality : 0.047 0.264 4588 Planarity : 0.005 0.067 4763 Dihedral : 15.692 177.692 4753 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.65 % Rotamer: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.13), residues: 3558 helix: -0.54 (0.14), residues: 1308 sheet: -1.37 (0.27), residues: 360 loop : -2.35 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 93 TYR 0.027 0.002 TYR F 153 PHE 0.051 0.003 PHE G 230 TRP 0.021 0.002 TRP C 39 HIS 0.012 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.27 (28095) covalent geometry : angle 0.75948 / 0.40 (38625) hydrogen bonds : bond 0.04121 / 2.86 ( 1020) hydrogen bonds : angle 5.23295 / 3.63 ( 2839) metal coordination : bond 0.00697 / 0.39 ( 6) metal coordination : angle 2.32471 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 568 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8647 (m-30) cc_final: 0.7983 (p0) REVERT: B 143 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 30 ILE cc_start: 0.8697 (mm) cc_final: 0.8297 (mm) REVERT: C 127 ILE cc_start: 0.9378 (mp) cc_final: 0.9083 (mt) REVERT: C 237 TYR cc_start: 0.7268 (t80) cc_final: 0.6550 (t80) REVERT: C 502 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8348 (pm20) REVERT: C 639 MET cc_start: 0.8258 (tpp) cc_final: 0.8051 (tpp) REVERT: C 719 ASN cc_start: 0.8468 (m-40) cc_final: 0.8134 (m-40) REVERT: C 744 ASP cc_start: 0.6384 (p0) cc_final: 0.6140 (p0) REVERT: C 764 MET cc_start: 0.9476 (ppp) cc_final: 0.8018 (ppp) REVERT: C 841 LEU cc_start: 0.9318 (tp) cc_final: 0.9005 (tp) REVERT: C 973 GLU cc_start: 0.8407 (pp20) cc_final: 0.8203 (pp20) REVERT: C 1073 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7394 (tm-30) REVERT: C 1079 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 1135 LEU cc_start: 0.9125 (mt) cc_final: 0.8533 (mt) REVERT: D 70 TYR cc_start: 0.6541 (m-80) cc_final: 0.6280 (m-10) REVERT: D 103 HIS cc_start: 0.7910 (t-90) cc_final: 0.7637 (t-90) REVERT: D 290 GLU cc_start: 0.8622 (pt0) cc_final: 0.8347 (pt0) REVERT: D 516 PHE cc_start: 0.8941 (m-80) cc_final: 0.8268 (m-80) REVERT: D 753 ASN cc_start: 0.7919 (m110) cc_final: 0.7672 (m110) REVERT: D 759 ILE cc_start: 0.7541 (mt) cc_final: 0.7248 (mt) REVERT: D 861 LEU cc_start: 0.8539 (pt) cc_final: 0.7926 (mt) REVERT: D 1077 LYS cc_start: 0.6915 (tptm) cc_final: 0.6308 (tptt) REVERT: D 1143 THR cc_start: 0.8963 (m) cc_final: 0.8283 (t) REVERT: D 1161 LEU cc_start: 0.6822 (pt) cc_final: 0.6133 (pt) REVERT: E 17 TYR cc_start: 0.7755 (m-80) cc_final: 0.6775 (m-80) REVERT: E 51 LEU cc_start: 0.8608 (mp) cc_final: 0.7647 (tt) REVERT: F 158 MET cc_start: 0.7660 (pmm) cc_final: 0.7158 (pmm) REVERT: F 191 THR cc_start: 0.9135 (t) cc_final: 0.8892 (p) REVERT: F 252 LYS cc_start: 0.9563 (tppt) cc_final: 0.8977 (tppp) REVERT: G 216 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7860 (ttp80) REVERT: G 268 TYR cc_start: 0.7434 (p90) cc_final: 0.7089 (p90) REVERT: I 16 ASN cc_start: 0.8502 (m110) cc_final: 0.8132 (m110) REVERT: I 133 ARG cc_start: 0.6791 (mtp180) cc_final: 0.6152 (mtp180) REVERT: I 207 MET cc_start: 0.6018 (mmp) cc_final: 0.5223 (mmm) REVERT: I 252 TYR cc_start: 0.8050 (m-80) cc_final: 0.7435 (m-10) REVERT: H 6 PHE cc_start: 0.8563 (m-10) cc_final: 0.8278 (m-10) outliers start: 3 outliers final: 2 residues processed: 570 average time/residue: 0.1596 time to fit residues: 150.7673 Evaluate side-chains 444 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 343 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 344 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 274 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS C 38 GLN C 128 ASN C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN C1136 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1066 HIS F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.116363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099150 restraints weight = 104321.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101527 restraints weight = 67632.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.103220 restraints weight = 47785.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.104420 restraints weight = 36266.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.105316 restraints weight = 29234.758| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28101 Z= 0.174 Angle : 0.649 15.708 38631 Z= 0.339 Chirality : 0.046 0.543 4588 Planarity : 0.004 0.059 4763 Dihedral : 15.664 177.913 4753 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.13), residues: 3558 helix: -0.52 (0.14), residues: 1331 sheet: -1.56 (0.26), residues: 368 loop : -2.27 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 345 TYR 0.018 0.002 TYR D 501 PHE 0.034 0.002 PHE F 369 TRP 0.019 0.002 TRP D 105 HIS 0.010 0.001 HIS F 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (28095) covalent geometry : angle 0.64908 / 0.34 (38625) hydrogen bonds : bond 0.03667 / 2.54 ( 1020) hydrogen bonds : angle 5.11441 / 3.56 ( 2839) metal coordination : bond 0.00292 / 0.15 ( 6) metal coordination : angle 1.50284 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 567 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8674 (m-30) cc_final: 0.8020 (p0) REVERT: B 80 LEU cc_start: 0.9155 (mp) cc_final: 0.8954 (mp) REVERT: B 143 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6805 (tm-30) REVERT: B 170 TYR cc_start: 0.6931 (m-80) cc_final: 0.6507 (m-80) REVERT: C 30 ILE cc_start: 0.8691 (mm) cc_final: 0.8177 (mm) REVERT: C 127 ILE cc_start: 0.9344 (mp) cc_final: 0.9068 (mt) REVERT: C 237 TYR cc_start: 0.7226 (t80) cc_final: 0.6489 (t80) REVERT: C 489 LEU cc_start: 0.7035 (mp) cc_final: 0.6661 (mp) REVERT: C 639 MET cc_start: 0.8220 (tpp) cc_final: 0.7786 (tpp) REVERT: C 719 ASN cc_start: 0.8413 (m-40) cc_final: 0.8088 (m-40) REVERT: C 764 MET cc_start: 0.9493 (ppp) cc_final: 0.8033 (ppp) REVERT: C 841 LEU cc_start: 0.9348 (tp) cc_final: 0.9040 (tp) REVERT: C 1012 ASP cc_start: 0.8283 (p0) cc_final: 0.7997 (p0) REVERT: C 1073 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 1079 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7622 (mt-10) REVERT: C 1135 LEU cc_start: 0.9130 (mt) cc_final: 0.8563 (mt) REVERT: D 175 ILE cc_start: 0.8210 (tt) cc_final: 0.8002 (tt) REVERT: D 290 GLU cc_start: 0.8618 (pt0) cc_final: 0.8273 (pt0) REVERT: D 516 PHE cc_start: 0.8859 (m-80) cc_final: 0.8354 (m-80) REVERT: D 753 ASN cc_start: 0.8044 (m110) cc_final: 0.7760 (m110) REVERT: D 759 ILE cc_start: 0.7661 (mt) cc_final: 0.7377 (mt) REVERT: D 861 LEU cc_start: 0.8449 (pt) cc_final: 0.7878 (mt) REVERT: D 1077 LYS cc_start: 0.6936 (tptm) cc_final: 0.6237 (tptt) REVERT: D 1161 LEU cc_start: 0.6744 (pt) cc_final: 0.5788 (pt) REVERT: E 17 TYR cc_start: 0.7851 (m-80) cc_final: 0.6919 (m-80) REVERT: E 51 LEU cc_start: 0.8548 (mp) cc_final: 0.7650 (tt) REVERT: E 62 GLU cc_start: 0.7756 (tp30) cc_final: 0.7466 (tt0) REVERT: F 158 MET cc_start: 0.7814 (pmm) cc_final: 0.7286 (pmm) REVERT: F 191 THR cc_start: 0.9107 (t) cc_final: 0.8854 (p) REVERT: F 252 LYS cc_start: 0.9554 (tppt) cc_final: 0.8983 (tppp) REVERT: F 304 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8350 (tp30) REVERT: F 344 GLU cc_start: 0.7930 (tp30) cc_final: 0.7139 (tp30) REVERT: G 191 PHE cc_start: 0.8312 (p90) cc_final: 0.7911 (p90) REVERT: G 216 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7781 (ttp80) REVERT: G 268 TYR cc_start: 0.7336 (p90) cc_final: 0.7059 (p90) REVERT: G 272 MET cc_start: 0.7603 (mmp) cc_final: 0.7344 (mmp) REVERT: I 16 ASN cc_start: 0.8500 (m110) cc_final: 0.8123 (m110) REVERT: I 92 ARG cc_start: 0.8703 (tpt170) cc_final: 0.8067 (mmm-85) REVERT: I 133 ARG cc_start: 0.6834 (mtp180) cc_final: 0.6124 (ptm160) REVERT: I 207 MET cc_start: 0.6032 (mmp) cc_final: 0.5363 (mmm) REVERT: I 252 TYR cc_start: 0.8004 (m-80) cc_final: 0.7391 (m-10) outliers start: 3 outliers final: 2 residues processed: 569 average time/residue: 0.1698 time to fit residues: 158.6068 Evaluate side-chains 455 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 175 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 347 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 355 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 248 optimal weight: 0.3980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 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 = 0.3905 r_free = 0.3905 target = 0.111718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094576 restraints weight = 104384.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096839 restraints weight = 67404.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.098492 restraints weight = 47865.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099642 restraints weight = 36289.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.100520 restraints weight = 29306.216| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 28101 Z= 0.243 Angle : 0.748 13.160 38631 Z= 0.391 Chirality : 0.047 0.282 4588 Planarity : 0.005 0.088 4763 Dihedral : 15.765 177.213 4753 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 0.13 % Allowed : 2.62 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.13), residues: 3558 helix: -0.61 (0.14), residues: 1325 sheet: -1.65 (0.26), residues: 370 loop : -2.23 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG C 434 TYR 0.028 0.002 TYR I 42 PHE 0.025 0.003 PHE F 178 TRP 0.024 0.002 TRP D 105 HIS 0.006 0.001 HIS D 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (28095) covalent geometry : angle 0.74787 / 0.39 (38625) hydrogen bonds : bond 0.04187 / 2.89 ( 1020) hydrogen bonds : angle 5.27178 / 3.67 ( 2839) metal coordination : bond 0.00415 / 0.22 ( 6) metal coordination : angle 1.91005 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 546 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8778 (m-30) cc_final: 0.7962 (p0) REVERT: B 143 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 170 TYR cc_start: 0.7421 (m-80) cc_final: 0.7213 (m-80) REVERT: C 30 ILE cc_start: 0.8811 (mm) cc_final: 0.8234 (mm) REVERT: C 113 MET cc_start: 0.7038 (pmm) cc_final: 0.6823 (pmm) REVERT: C 127 ILE cc_start: 0.9398 (mp) cc_final: 0.9097 (mt) REVERT: C 237 TYR cc_start: 0.7337 (t80) cc_final: 0.6542 (t80) REVERT: C 489 LEU cc_start: 0.7209 (mp) cc_final: 0.6639 (mp) REVERT: C 639 MET cc_start: 0.8140 (tpp) cc_final: 0.7879 (tpp) REVERT: C 719 ASN cc_start: 0.8507 (m-40) cc_final: 0.8140 (m-40) REVERT: C 764 MET cc_start: 0.9007 (ppp) cc_final: 0.8028 (ppp) REVERT: C 841 LEU cc_start: 0.9425 (tp) cc_final: 0.9156 (tp) REVERT: C 935 ILE cc_start: 0.9260 (mm) cc_final: 0.8966 (mm) REVERT: C 1012 ASP cc_start: 0.8545 (p0) cc_final: 0.8181 (p0) REVERT: C 1017 LEU cc_start: 0.8861 (mp) cc_final: 0.8620 (mp) REVERT: C 1026 PHE cc_start: 0.7659 (m-80) cc_final: 0.7381 (m-80) REVERT: C 1079 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7781 (mt-10) REVERT: C 1135 LEU cc_start: 0.9155 (mt) cc_final: 0.8657 (mt) REVERT: C 1140 MET cc_start: 0.8768 (mpp) cc_final: 0.8471 (mpp) REVERT: D 287 MET cc_start: 0.9061 (ptp) cc_final: 0.8419 (ptp) REVERT: D 290 GLU cc_start: 0.8649 (pt0) cc_final: 0.8386 (pt0) REVERT: D 419 HIS cc_start: 0.7250 (p-80) cc_final: 0.7049 (p-80) REVERT: D 516 PHE cc_start: 0.8864 (m-80) cc_final: 0.8358 (m-80) REVERT: D 617 LYS cc_start: 0.8316 (tttp) cc_final: 0.8049 (tptp) REVERT: D 753 ASN cc_start: 0.8140 (m110) cc_final: 0.7835 (m110) REVERT: D 861 LEU cc_start: 0.8554 (pt) cc_final: 0.7921 (mt) REVERT: D 1077 LYS cc_start: 0.7093 (tptm) cc_final: 0.6821 (tptp) REVERT: E 51 LEU cc_start: 0.8624 (mp) cc_final: 0.7728 (tt) REVERT: E 62 GLU cc_start: 0.8063 (tp30) cc_final: 0.7704 (tt0) REVERT: F 158 MET cc_start: 0.8012 (pmm) cc_final: 0.7176 (pmm) REVERT: F 161 LEU cc_start: 0.9182 (tp) cc_final: 0.8783 (tp) REVERT: F 191 THR cc_start: 0.9163 (t) cc_final: 0.8890 (p) REVERT: F 252 LYS cc_start: 0.9592 (tppt) cc_final: 0.9032 (tppp) REVERT: F 337 LYS cc_start: 0.8922 (mtpp) cc_final: 0.8199 (ttpt) REVERT: G 191 PHE cc_start: 0.8428 (p90) cc_final: 0.7982 (p90) REVERT: G 216 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7654 (ttp80) REVERT: G 268 TYR cc_start: 0.7650 (p90) cc_final: 0.7325 (p90) REVERT: I 16 ASN cc_start: 0.8572 (m110) cc_final: 0.8205 (m110) REVERT: I 92 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8088 (mmm-85) REVERT: I 133 ARG cc_start: 0.6770 (mtp180) cc_final: 0.6080 (mtp180) REVERT: I 207 MET cc_start: 0.6439 (mmp) cc_final: 0.5624 (mmm) REVERT: I 252 TYR cc_start: 0.8179 (m-80) cc_final: 0.7606 (m-80) REVERT: H 33 VAL cc_start: 0.9580 (t) cc_final: 0.9351 (p) outliers start: 3 outliers final: 2 residues processed: 548 average time/residue: 0.1722 time to fit residues: 154.9810 Evaluate side-chains 424 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 422 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 113 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN A 154 ASN B 63 HIS ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.113196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096289 restraints weight = 106029.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098497 restraints weight = 69164.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100082 restraints weight = 49297.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101229 restraints weight = 37738.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102070 restraints weight = 30614.357| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28101 Z= 0.157 Angle : 0.666 10.983 38631 Z= 0.348 Chirality : 0.047 0.472 4588 Planarity : 0.005 0.073 4763 Dihedral : 15.726 177.913 4753 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 0.21 % Allowed : 1.60 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3558 helix: -0.44 (0.14), residues: 1329 sheet: -1.71 (0.26), residues: 359 loop : -2.16 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 267 TYR 0.049 0.002 TYR H 7 PHE 0.027 0.002 PHE I 158 TRP 0.013 0.001 TRP D 705 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (28095) covalent geometry : angle 0.66512 / 0.35 (38625) hydrogen bonds : bond 0.03532 / 2.44 ( 1020) hydrogen bonds : angle 5.07018 / 3.52 ( 2839) metal coordination : bond 0.00236 / 0.12 ( 6) metal coordination : angle 2.04517 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 544 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8763 (m-30) cc_final: 0.7940 (p0) REVERT: A 178 TYR cc_start: 0.8133 (p90) cc_final: 0.7923 (p90) REVERT: C 30 ILE cc_start: 0.8836 (mm) cc_final: 0.8276 (mm) REVERT: C 113 MET cc_start: 0.7108 (pmm) cc_final: 0.6762 (pmm) REVERT: C 127 ILE cc_start: 0.9351 (mp) cc_final: 0.9085 (mt) REVERT: C 237 TYR cc_start: 0.7397 (t80) cc_final: 0.6620 (t80) REVERT: C 476 PRO cc_start: 0.8930 (Cg_exo) cc_final: 0.8575 (Cg_endo) REVERT: C 719 ASN cc_start: 0.8442 (m-40) cc_final: 0.8066 (m-40) REVERT: C 764 MET cc_start: 0.9001 (ppp) cc_final: 0.8152 (ppp) REVERT: C 841 LEU cc_start: 0.9413 (tp) cc_final: 0.9103 (tp) REVERT: C 1012 ASP cc_start: 0.8458 (p0) cc_final: 0.8077 (p0) REVERT: C 1073 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7323 (tm-30) REVERT: C 1079 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 1135 LEU cc_start: 0.9180 (mt) cc_final: 0.8519 (mt) REVERT: C 1140 MET cc_start: 0.8708 (mpp) cc_final: 0.8302 (mpp) REVERT: D 105 TRP cc_start: 0.8753 (m-10) cc_final: 0.8484 (m-10) REVERT: D 287 MET cc_start: 0.8841 (ptp) cc_final: 0.8392 (ptp) REVERT: D 290 GLU cc_start: 0.8653 (pt0) cc_final: 0.8326 (pt0) REVERT: D 419 HIS cc_start: 0.7084 (p-80) cc_final: 0.6810 (p-80) REVERT: D 455 MET cc_start: 0.7103 (ptm) cc_final: 0.6846 (ptm) REVERT: D 499 ASN cc_start: 0.8917 (m110) cc_final: 0.8624 (m110) REVERT: D 501 TYR cc_start: 0.7597 (t80) cc_final: 0.6986 (t80) REVERT: D 516 PHE cc_start: 0.8792 (m-80) cc_final: 0.8314 (m-80) REVERT: D 617 LYS cc_start: 0.8258 (tttp) cc_final: 0.8023 (tptp) REVERT: D 641 ASP cc_start: 0.8163 (t0) cc_final: 0.7950 (t0) REVERT: D 753 ASN cc_start: 0.8269 (m110) cc_final: 0.7753 (m110) REVERT: D 759 ILE cc_start: 0.7963 (mt) cc_final: 0.7408 (mm) REVERT: D 861 LEU cc_start: 0.8386 (pt) cc_final: 0.7753 (mt) REVERT: D 1163 GLU cc_start: 0.6072 (pp20) cc_final: 0.5455 (tm-30) REVERT: E 51 LEU cc_start: 0.8611 (mp) cc_final: 0.7762 (tt) REVERT: E 62 GLU cc_start: 0.8021 (tp30) cc_final: 0.7647 (tt0) REVERT: F 158 MET cc_start: 0.8099 (pmm) cc_final: 0.7652 (pmm) REVERT: F 161 LEU cc_start: 0.9178 (tp) cc_final: 0.8897 (tp) REVERT: F 191 THR cc_start: 0.9122 (t) cc_final: 0.8829 (p) REVERT: F 252 LYS cc_start: 0.9590 (tppt) cc_final: 0.9046 (tppp) REVERT: F 304 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8399 (tp30) REVERT: F 337 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8164 (ttpt) REVERT: G 191 PHE cc_start: 0.8387 (p90) cc_final: 0.7953 (p90) REVERT: G 216 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7566 (ttp80) REVERT: G 268 TYR cc_start: 0.7352 (p90) cc_final: 0.7077 (p90) REVERT: I 16 ASN cc_start: 0.8626 (m110) cc_final: 0.8248 (m110) REVERT: I 25 TYR cc_start: 0.8688 (m-80) cc_final: 0.8387 (m-80) REVERT: I 92 ARG cc_start: 0.8666 (tpt170) cc_final: 0.7992 (mmm-85) REVERT: I 133 ARG cc_start: 0.6677 (mtp180) cc_final: 0.6063 (mtp180) REVERT: I 252 TYR cc_start: 0.8097 (m-80) cc_final: 0.7542 (m-80) REVERT: H 7 TYR cc_start: 0.7348 (p90) cc_final: 0.6692 (p90) REVERT: H 33 VAL cc_start: 0.9590 (t) cc_final: 0.9359 (p) outliers start: 5 outliers final: 3 residues processed: 547 average time/residue: 0.1711 time to fit residues: 152.7652 Evaluate side-chains 434 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 431 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 205 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 357 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 253 optimal weight: 20.0000 chunk 80 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 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 = 0.3928 r_free = 0.3928 target = 0.112845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096001 restraints weight = 105120.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098239 restraints weight = 68454.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099812 restraints weight = 48567.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.100957 restraints weight = 37070.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.101790 restraints weight = 29989.616| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28101 Z= 0.150 Angle : 0.654 9.880 38631 Z= 0.340 Chirality : 0.046 0.271 4588 Planarity : 0.005 0.065 4763 Dihedral : 15.703 177.424 4753 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.91 % Favored : 93.06 % Rotamer: Outliers : 0.08 % Allowed : 0.68 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3558 helix: -0.36 (0.14), residues: 1336 sheet: -1.62 (0.26), residues: 377 loop : -2.07 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 34 TYR 0.025 0.002 TYR H 7 PHE 0.018 0.002 PHE G 230 TRP 0.011 0.001 TRP D 705 HIS 0.007 0.001 HIS F 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (28095) covalent geometry : angle 0.65372 / 0.34 (38625) hydrogen bonds : bond 0.03425 / 2.38 ( 1020) hydrogen bonds : angle 5.01494 / 3.48 ( 2839) metal coordination : bond 0.00202 / 0.10 ( 6) metal coordination : angle 1.84909 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 549 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8679 (m-30) cc_final: 0.7946 (p0) REVERT: C 30 ILE cc_start: 0.8793 (mm) cc_final: 0.8350 (mm) REVERT: C 92 LEU cc_start: 0.8034 (tp) cc_final: 0.7711 (tp) REVERT: C 113 MET cc_start: 0.7303 (pmm) cc_final: 0.6810 (pmm) REVERT: C 127 ILE cc_start: 0.9325 (mp) cc_final: 0.9058 (mt) REVERT: C 237 TYR cc_start: 0.7433 (t80) cc_final: 0.6659 (t80) REVERT: C 476 PRO cc_start: 0.8882 (Cg_exo) cc_final: 0.8488 (Cg_endo) REVERT: C 479 GLU cc_start: 0.8855 (tt0) cc_final: 0.8489 (tt0) REVERT: C 639 MET cc_start: 0.8487 (tpp) cc_final: 0.8163 (tpp) REVERT: C 669 ASP cc_start: 0.8019 (p0) cc_final: 0.6672 (t70) REVERT: C 764 MET cc_start: 0.8988 (ppp) cc_final: 0.8114 (ppp) REVERT: C 841 LEU cc_start: 0.9406 (tp) cc_final: 0.9086 (tp) REVERT: C 932 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7629 (tppt) REVERT: C 1012 ASP cc_start: 0.8450 (p0) cc_final: 0.8199 (p0) REVERT: C 1017 LEU cc_start: 0.8793 (mp) cc_final: 0.8593 (mp) REVERT: C 1026 PHE cc_start: 0.7407 (m-80) cc_final: 0.7070 (m-80) REVERT: C 1079 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7758 (mt-10) REVERT: C 1135 LEU cc_start: 0.9133 (mt) cc_final: 0.8660 (mt) REVERT: D 287 MET cc_start: 0.8807 (ptp) cc_final: 0.8302 (ptp) REVERT: D 290 GLU cc_start: 0.8632 (pt0) cc_final: 0.8416 (pt0) REVERT: D 455 MET cc_start: 0.7018 (ptm) cc_final: 0.6744 (ptm) REVERT: D 499 ASN cc_start: 0.8867 (m110) cc_final: 0.8648 (m110) REVERT: D 516 PHE cc_start: 0.8819 (m-80) cc_final: 0.8445 (m-80) REVERT: D 753 ASN cc_start: 0.8230 (m110) cc_final: 0.7660 (m110) REVERT: D 759 ILE cc_start: 0.7979 (mt) cc_final: 0.7646 (mm) REVERT: D 861 LEU cc_start: 0.8381 (pt) cc_final: 0.7633 (mt) REVERT: D 1163 GLU cc_start: 0.6059 (pp20) cc_final: 0.5407 (tm-30) REVERT: E 7 ASP cc_start: 0.8886 (t70) cc_final: 0.8500 (t70) REVERT: E 51 LEU cc_start: 0.8639 (mp) cc_final: 0.7812 (tt) REVERT: E 62 GLU cc_start: 0.8051 (tp30) cc_final: 0.7694 (tt0) REVERT: F 158 MET cc_start: 0.8084 (pmm) cc_final: 0.7356 (pmm) REVERT: F 161 LEU cc_start: 0.9142 (tp) cc_final: 0.8820 (tp) REVERT: F 191 THR cc_start: 0.9140 (t) cc_final: 0.8850 (p) REVERT: F 252 LYS cc_start: 0.9575 (tppt) cc_final: 0.9014 (tppp) REVERT: F 337 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8143 (ttpt) REVERT: F 344 GLU cc_start: 0.7902 (tp30) cc_final: 0.6774 (tt0) REVERT: G 191 PHE cc_start: 0.8287 (p90) cc_final: 0.7848 (p90) REVERT: G 216 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7518 (ttp80) REVERT: G 268 TYR cc_start: 0.7364 (p90) cc_final: 0.7092 (p90) REVERT: G 272 MET cc_start: 0.7932 (mmp) cc_final: 0.7724 (mmp) REVERT: I 16 ASN cc_start: 0.8603 (m110) cc_final: 0.8234 (m110) REVERT: I 25 TYR cc_start: 0.8659 (m-80) cc_final: 0.8350 (m-80) REVERT: I 52 HIS cc_start: 0.9190 (m90) cc_final: 0.8751 (m-70) REVERT: I 92 ARG cc_start: 0.8654 (tpt170) cc_final: 0.7973 (mmm-85) REVERT: I 111 ARG cc_start: 0.8305 (ptt180) cc_final: 0.7283 (ttp80) REVERT: I 133 ARG cc_start: 0.6626 (mtp180) cc_final: 0.6013 (mtp180) REVERT: I 185 MET cc_start: 0.4392 (ptp) cc_final: 0.4044 (pmm) REVERT: I 207 MET cc_start: 0.6253 (mmp) cc_final: 0.3409 (tmm) REVERT: I 252 TYR cc_start: 0.8110 (m-80) cc_final: 0.7530 (m-80) REVERT: H 33 VAL cc_start: 0.9568 (t) cc_final: 0.9348 (p) outliers start: 2 outliers final: 2 residues processed: 551 average time/residue: 0.1682 time to fit residues: 152.5988 Evaluate side-chains 430 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 1 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 chunk 161 optimal weight: 50.0000 chunk 356 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 220 HIS C 406 ASN C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** C 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.108174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091337 restraints weight = 107282.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093456 restraints weight = 70015.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094968 restraints weight = 49878.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096044 restraints weight = 38276.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096846 restraints weight = 31154.643| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 28101 Z= 0.239 Angle : 0.764 13.665 38631 Z= 0.398 Chirality : 0.048 0.304 4588 Planarity : 0.005 0.089 4763 Dihedral : 15.838 175.807 4753 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.27 % Rotamer: Outliers : 0.13 % Allowed : 0.84 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 3558 helix: -0.47 (0.14), residues: 1322 sheet: -1.62 (0.26), residues: 362 loop : -2.15 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 434 TYR 0.029 0.002 TYR D 106 PHE 0.027 0.003 PHE D 107 TRP 0.022 0.003 TRP D 105 HIS 0.008 0.002 HIS F 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (28095) covalent geometry : angle 0.76323 / 0.40 (38625) hydrogen bonds : bond 0.04229 / 2.92 ( 1020) hydrogen bonds : angle 5.31977 / 3.68 ( 2839) metal coordination : bond 0.00493 / 0.25 ( 6) metal coordination : angle 2.58034 / 1.38 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 540 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.6785 (pm20) cc_final: 0.5690 (pm20) REVERT: A 167 ASP cc_start: 0.8810 (m-30) cc_final: 0.7984 (p0) REVERT: C 30 ILE cc_start: 0.8953 (mm) cc_final: 0.8466 (mm) REVERT: C 92 LEU cc_start: 0.8207 (tp) cc_final: 0.7844 (tp) REVERT: C 113 MET cc_start: 0.7233 (pmm) cc_final: 0.6733 (pmm) REVERT: C 127 ILE cc_start: 0.9439 (mp) cc_final: 0.9212 (mt) REVERT: C 476 PRO cc_start: 0.9113 (Cg_exo) cc_final: 0.8755 (Cg_endo) REVERT: C 479 GLU cc_start: 0.8940 (tt0) cc_final: 0.8661 (tt0) REVERT: C 764 MET cc_start: 0.8951 (ppp) cc_final: 0.8163 (ppp) REVERT: C 841 LEU cc_start: 0.9441 (tp) cc_final: 0.9158 (tp) REVERT: C 1012 ASP cc_start: 0.8534 (p0) cc_final: 0.8111 (p0) REVERT: C 1017 LEU cc_start: 0.8844 (mp) cc_final: 0.8603 (mp) REVERT: C 1035 MET cc_start: 0.7367 (mmm) cc_final: 0.6817 (mmm) REVERT: C 1079 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 1135 LEU cc_start: 0.9191 (mt) cc_final: 0.8502 (mt) REVERT: C 1140 MET cc_start: 0.8712 (mpp) cc_final: 0.8374 (mpp) REVERT: D 31 PRO cc_start: 0.8522 (Cg_exo) cc_final: 0.8186 (Cg_endo) REVERT: D 33 THR cc_start: 0.9217 (p) cc_final: 0.8874 (t) REVERT: D 210 LEU cc_start: 0.7909 (mt) cc_final: 0.7453 (mt) REVERT: D 290 GLU cc_start: 0.8711 (pt0) cc_final: 0.8451 (pt0) REVERT: D 419 HIS cc_start: 0.7401 (p-80) cc_final: 0.7197 (p-80) REVERT: D 499 ASN cc_start: 0.9203 (m110) cc_final: 0.8997 (m110) REVERT: D 516 PHE cc_start: 0.8812 (m-80) cc_final: 0.8468 (m-80) REVERT: D 641 ASP cc_start: 0.8072 (t0) cc_final: 0.7809 (t0) REVERT: D 753 ASN cc_start: 0.8322 (m110) cc_final: 0.7974 (m110) REVERT: D 759 ILE cc_start: 0.8029 (mt) cc_final: 0.7820 (mt) REVERT: D 861 LEU cc_start: 0.8439 (pt) cc_final: 0.7660 (mt) REVERT: D 1163 GLU cc_start: 0.6498 (pp20) cc_final: 0.5868 (tm-30) REVERT: E 7 ASP cc_start: 0.8998 (t70) cc_final: 0.8620 (t70) REVERT: E 51 LEU cc_start: 0.8819 (mp) cc_final: 0.8019 (tt) REVERT: F 158 MET cc_start: 0.8266 (pmm) cc_final: 0.7552 (pmm) REVERT: F 191 THR cc_start: 0.9156 (t) cc_final: 0.8866 (p) REVERT: F 252 LYS cc_start: 0.9587 (tppt) cc_final: 0.9039 (tppp) REVERT: F 267 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7543 (mm-30) REVERT: F 333 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6722 (mm-30) REVERT: F 337 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8358 (ttpt) REVERT: G 216 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7588 (mtm110) REVERT: G 268 TYR cc_start: 0.7699 (p90) cc_final: 0.7323 (p90) REVERT: I 16 ASN cc_start: 0.8653 (m110) cc_final: 0.8295 (m110) REVERT: I 25 TYR cc_start: 0.8674 (m-80) cc_final: 0.8384 (m-80) REVERT: I 52 HIS cc_start: 0.9198 (m90) cc_final: 0.8771 (m-70) REVERT: I 92 ARG cc_start: 0.8696 (tpt170) cc_final: 0.8029 (mmm-85) REVERT: I 133 ARG cc_start: 0.6680 (mtp180) cc_final: 0.5933 (mtp180) REVERT: I 207 MET cc_start: 0.6536 (mmp) cc_final: 0.5736 (mmm) REVERT: I 252 TYR cc_start: 0.8084 (m-80) cc_final: 0.7450 (m-10) REVERT: H 7 TYR cc_start: 0.7342 (p90) cc_final: 0.6767 (p90) outliers start: 3 outliers final: 2 residues processed: 542 average time/residue: 0.1599 time to fit residues: 143.4134 Evaluate side-chains 432 residues out of total 3126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 430 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 35 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS B 63 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN C 719 ASN C 720 GLN ** C 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1066 HIS F 142 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 197 ASN G 259 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.108024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091344 restraints weight = 106036.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093455 restraints weight = 68703.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095004 restraints weight = 48771.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096097 restraints weight = 37040.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096801 restraints weight = 30019.233| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28101 Z= 0.194 Angle : 0.704 11.309 38631 Z= 0.368 Chirality : 0.047 0.261 4588 Planarity : 0.005 0.068 4763 Dihedral : 15.836 178.721 4753 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.50 % Rotamer: Outliers : 0.13 % Allowed : 0.84 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3558 helix: -0.37 (0.14), residues: 1317 sheet: -1.62 (0.27), residues: 350 loop : -2.05 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 23 TYR 0.025 0.002 TYR G 35 PHE 0.041 0.002 PHE C 470 TRP 0.035 0.002 TRP D 105 HIS 0.008 0.001 HIS F 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (28095) covalent geometry : angle 0.70374 / 0.37 (38625) hydrogen bonds : bond 0.03845 / 2.67 ( 1020) hydrogen bonds : angle 5.19719 / 3.59 ( 2839) metal coordination : bond 0.00417 / 0.21 ( 6) metal coordination : angle 2.45495 / 1.30 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5080.76 seconds wall clock time: 88 minutes 18.60 seconds (5298.60 seconds total)