Starting phenix.real_space_refine on Mon Sep 14 02:49:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.map" model { file = "/net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6r5k_4728/09_2026/6r5k_4728.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4894 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 67 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 14642 2.51 5 N 4061 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s 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: 23508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8053 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 996} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 9, 'ARG:plan': 7, 'TYR:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "D" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2984 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 379} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 3, 'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1474 Classifications: {'RNAv2': 67} Modifications used: {'rna2p_pur': 42, 'rna3p_pur': 25} Link IDs: {'rna2p': 41, 'rna3p': 25} Chain: "F" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1241 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 159} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3052 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 383} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "N" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3282 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 3 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 10, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "O" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3420 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'HIS:plan': 4, 'GLU:plan': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 6, 'ARG:plan': 4, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 133 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.07, per 1000 atoms: 0.22 Number of scatterers: 23508 At special positions: 0 Unit cell: (141.504, 139.392, 181.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 67 15.00 Mg 2 11.99 O 4649 8.00 N 4061 7.00 C 14642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 28 sheets defined 33.5% alpha, 12.7% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 515 through 524 removed outlier: 4.125A pdb=" N ILE A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 544 through 561 removed outlier: 4.207A pdb=" N HIS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 695 through 704 removed outlier: 3.560A pdb=" N LYS A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 752 removed outlier: 3.607A pdb=" N PHE A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 896 through 900 removed outlier: 3.537A pdb=" N ALA A 900 " --> pdb=" O HIS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1009 removed outlier: 3.818A pdb=" N GLY A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1025 removed outlier: 3.818A pdb=" N ASP A1020 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1034 removed outlier: 4.665A pdb=" N ARG A1034 " --> pdb=" O ARG A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 removed outlier: 3.749A pdb=" N PHE A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1057 removed outlier: 3.926A pdb=" N LEU A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1088 Processing helix chain 'A' and resid 1090 through 1105 removed outlier: 4.007A pdb=" N VAL A1094 " --> pdb=" O ILE A1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 59 removed outlier: 3.980A pdb=" N LEU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.619A pdb=" N GLY D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.954A pdb=" N LYS D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 124' Processing helix chain 'D' and resid 138 through 147 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.853A pdb=" N PHE D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 278 removed outlier: 3.507A pdb=" N ALA D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 320 removed outlier: 4.008A pdb=" N LYS D 306 " --> pdb=" O HIS D 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN D 320 " --> pdb=" O MET D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 343 through 346 removed outlier: 4.039A pdb=" N GLY D 346 " --> pdb=" O ALA D 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 343 through 346' Processing helix chain 'D' and resid 371 through 382 Processing helix chain 'D' and resid 401 through 426 removed outlier: 3.514A pdb=" N SER D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.638A pdb=" N PHE F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 62 removed outlier: 3.784A pdb=" N GLY F 62 " --> pdb=" O SER F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 59 through 62' Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.553A pdb=" N GLY F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 177 through 187 Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 138 through 146 Processing helix chain 'H' and resid 175 through 186 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 233 through 238 removed outlier: 4.584A pdb=" N LEU H 238 " --> pdb=" O GLN H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 243 removed outlier: 3.761A pdb=" N GLY H 243 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 277 Processing helix chain 'H' and resid 304 through 312 removed outlier: 3.625A pdb=" N TYR H 308 " --> pdb=" O LEU H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 343 Processing helix chain 'H' and resid 344 through 346 No H-bonds generated for 'chain 'H' and resid 344 through 346' Processing helix chain 'H' and resid 371 through 381 removed outlier: 3.581A pdb=" N ALA H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 427 Processing helix chain 'N' and resid 261 through 275 removed outlier: 3.983A pdb=" N GLN N 275 " --> pdb=" O LEU N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 348 Processing helix chain 'N' and resid 383 through 389 Processing helix chain 'N' and resid 398 through 419 removed outlier: 3.690A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 449 through 453 Processing helix chain 'N' and resid 467 through 493 Processing helix chain 'N' and resid 508 through 514 Processing helix chain 'N' and resid 519 through 531 Processing helix chain 'N' and resid 539 through 548 Processing helix chain 'N' and resid 549 through 570 removed outlier: 3.544A pdb=" N MET N 553 " --> pdb=" O ASP N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 575 through 588 removed outlier: 4.283A pdb=" N ILE N 588 " --> pdb=" O LYS N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 601 removed outlier: 3.912A pdb=" N TRP N 600 " --> pdb=" O ASP N 597 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER N 601 " --> pdb=" O ILE N 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 597 through 601' Processing helix chain 'N' and resid 607 through 618 removed outlier: 3.620A pdb=" N LEU N 611 " --> pdb=" O PHE N 607 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR N 613 " --> pdb=" O ILE N 609 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE N 617 " --> pdb=" O TYR N 613 " (cutoff:3.500A) Processing helix chain 'N' and resid 629 through 643 removed outlier: 3.556A pdb=" N VAL N 633 " --> pdb=" O ASP N 629 " (cutoff:3.500A) Processing helix chain 'N' and resid 663 through 679 Processing helix chain 'O' and resid 240 through 245 removed outlier: 3.873A pdb=" N LEU O 245 " --> pdb=" O SER O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 257 Processing helix chain 'O' and resid 259 through 274 removed outlier: 3.876A pdb=" N ARG O 263 " --> pdb=" O PRO O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 348 removed outlier: 4.217A pdb=" N ILE O 339 " --> pdb=" O ASN O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 384 through 389 Processing helix chain 'O' and resid 398 through 420 Processing helix chain 'O' and resid 468 through 493 removed outlier: 5.297A pdb=" N TYR O 476 " --> pdb=" O GLN O 472 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS O 477 " --> pdb=" O GLN O 473 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU O 491 " --> pdb=" O SER O 487 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN O 492 " --> pdb=" O ILE O 488 " (cutoff:3.500A) Processing helix chain 'O' and resid 508 through 515 Processing helix chain 'O' and resid 519 through 529 Processing helix chain 'O' and resid 548 through 589 removed outlier: 4.521A pdb=" N ILE O 588 " --> pdb=" O LYS O 584 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE O 589 " --> pdb=" O LEU O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 605 through 611 Processing helix chain 'O' and resid 612 through 618 Processing helix chain 'O' and resid 629 through 643 removed outlier: 3.927A pdb=" N ALA O 642 " --> pdb=" O ASN O 638 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY O 643 " --> pdb=" O LYS O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 663 through 678 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.044A pdb=" N ILE A 53 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG A 65 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER A 55 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 5.983A pdb=" N ASN A 97 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR A 102 " --> pdb=" O ASN A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.555A pdb=" N GLY A 175 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 193 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 208 removed outlier: 5.361A pdb=" N VAL A 232 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP A 234 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN A 240 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA8, first strand: chain 'A' and resid 664 through 670 Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675 removed outlier: 6.880A pdb=" N GLU A 848 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 793 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 850 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY A 791 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 852 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 789 " --> pdb=" O TYR A 852 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 675 removed outlier: 6.880A pdb=" N GLU A 848 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 793 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 850 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY A 791 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 852 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 789 " --> pdb=" O TYR A 852 " (cutoff:3.500A) removed outlier: 14.111A pdb=" N GLU A 788 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N TYR A 812 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASN A 790 " --> pdb=" O LYS A 810 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP A 821 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 990 through 992 removed outlier: 9.201A pdb=" N LYS A 990 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP A 959 " --> pdb=" O LYS A 990 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 992 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR A 961 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 944 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 959 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 942 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR A 961 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA A 940 " --> pdb=" O TYR A 961 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU A 912 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE A 942 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP A 910 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 944 " --> pdb=" O ALA A 908 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 908 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 905 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A1013 " --> pdb=" O THR A 905 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 907 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.823A pdb=" N SER D 66 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR D 83 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG D 68 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR D 81 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N CYS D 70 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 103 through 104 removed outlier: 4.100A pdb=" N ARG D 107 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.585A pdb=" N GLY D 169 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 222 through 224 removed outlier: 3.767A pdb=" N TYR D 222 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 247 through 249 removed outlier: 3.958A pdb=" N SER D 247 " --> pdb=" O ASN D 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 364 through 368 Processing sheet with id=AB9, first strand: chain 'F' and resid 66 through 68 Processing sheet with id=AC1, first strand: chain 'F' and resid 128 through 130 removed outlier: 7.013A pdb=" N ALA F 158 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE F 168 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS F 156 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE F 170 " --> pdb=" O SER F 154 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER F 154 " --> pdb=" O PHE F 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 64 through 68 Processing sheet with id=AC3, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'H' and resid 103 through 104 removed outlier: 3.580A pdb=" N ARG H 107 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.220A pdb=" N SER H 249 " --> pdb=" O PHE H 263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE H 263 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR H 290 " --> pdb=" O LYS H 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 350 through 353 removed outlier: 4.269A pdb=" N PHE H 325 " --> pdb=" O ALA H 395 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA H 395 " --> pdb=" O PHE H 325 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 291 through 296 removed outlier: 5.061A pdb=" N ASN N 293 " --> pdb=" O PHE N 314 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE N 314 " --> pdb=" O ASN N 293 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP N 359 " --> pdb=" O VAL N 374 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 291 through 296 removed outlier: 5.310A pdb=" N ASN O 293 " --> pdb=" O PHE O 314 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE O 314 " --> pdb=" O ASN O 293 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER O 370 " --> pdb=" O GLN O 362 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN O 362 " --> pdb=" O SER O 370 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS O 372 " --> pdb=" O ILE O 360 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE O 360 " --> pdb=" O CYS O 372 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 647 through 651 815 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6837 1.34 - 1.46: 5928 1.46 - 1.58: 11118 1.58 - 1.71: 133 1.71 - 1.83: 133 Bond restraints: 24149 Sorted by residual: bond pdb=" C ARG F 116 " pdb=" O ARG F 116 " ideal model delta sigma weight residual 1.244 1.212 0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N MET H 301 " pdb=" CA MET H 301 " ideal model delta sigma weight residual 1.458 1.498 -0.039 1.61e-02 3.86e+03 6.00e+00 bond pdb=" C ASP A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.00e+00 bond pdb=" CG1 ILE H 245 " pdb=" CD1 ILE H 245 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.68e+00 bond pdb=" C HIS F 134 " pdb=" N PRO F 135 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.60e+00 ... (remaining 24144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 32335 3.36 - 6.72: 671 6.72 - 10.08: 80 10.08 - 13.44: 10 13.44 - 16.79: 2 Bond angle restraints: 33098 Sorted by residual: angle pdb=" N PRO O 225 " pdb=" CA PRO O 225 " pdb=" CB PRO O 225 " ideal model delta sigma weight residual 103.25 111.40 -8.15 1.05e+00 9.07e-01 6.02e+01 angle pdb=" N PRO D 200 " pdb=" CA PRO D 200 " pdb=" CB PRO D 200 " ideal model delta sigma weight residual 103.25 110.90 -7.65 1.05e+00 9.07e-01 5.31e+01 angle pdb=" N PRO A 338 " pdb=" CA PRO A 338 " pdb=" CB PRO A 338 " ideal model delta sigma weight residual 103.25 110.88 -7.63 1.05e+00 9.07e-01 5.28e+01 angle pdb=" N PRO F 118 " pdb=" CA PRO F 118 " pdb=" CB PRO F 118 " ideal model delta sigma weight residual 103.20 109.99 -6.79 9.50e-01 1.11e+00 5.11e+01 angle pdb=" N PRO O 224 " pdb=" CA PRO O 224 " pdb=" CB PRO O 224 " ideal model delta sigma weight residual 103.00 110.66 -7.66 1.10e+00 8.26e-01 4.85e+01 ... (remaining 33093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 13886 35.90 - 71.80: 359 71.80 - 107.70: 29 107.70 - 143.59: 1 143.59 - 179.49: 3 Dihedral angle restraints: 14278 sinusoidal: 5860 harmonic: 8418 Sorted by residual: dihedral pdb=" C4' A E 33 " pdb=" C3' A E 33 " pdb=" C2' A E 33 " pdb=" C1' A E 33 " ideal model delta sinusoidal sigma weight residual 36.34 -41.97 78.31 1 3.10e+00 1.04e-01 7.97e+02 dihedral pdb=" C4' A E 65 " pdb=" C3' A E 65 " pdb=" C2' A E 65 " pdb=" C1' A E 65 " ideal model delta sinusoidal sigma weight residual 36.34 -41.24 77.58 1 3.10e+00 1.04e-01 7.84e+02 dihedral pdb=" C4' A E 64 " pdb=" C3' A E 64 " pdb=" C2' A E 64 " pdb=" C1' A E 64 " ideal model delta sinusoidal sigma weight residual 36.35 -39.82 76.17 1 3.10e+00 1.04e-01 7.60e+02 ... (remaining 14275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3125 0.088 - 0.177: 443 0.177 - 0.265: 124 0.265 - 0.354: 67 0.354 - 0.442: 3 Chirality restraints: 3762 Sorted by residual: chirality pdb=" P A E 65 " pdb=" OP1 A E 65 " pdb=" OP2 A E 65 " pdb=" O5' A E 65 " both_signs ideal model delta sigma weight residual True 2.17 -2.62 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" P A E 58 " pdb=" OP1 A E 58 " pdb=" OP2 A E 58 " pdb=" O5' A E 58 " both_signs ideal model delta sigma weight residual True 2.17 -2.61 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB ILE N 596 " pdb=" CA ILE N 596 " pdb=" CG1 ILE N 596 " pdb=" CG2 ILE N 596 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 3759 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG H 300 " 0.034 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C ARG H 300 " -0.116 2.00e-02 2.50e+03 pdb=" O ARG H 300 " 0.044 2.00e-02 2.50e+03 pdb=" N MET H 301 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 101 " -0.027 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR H 101 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR H 101 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR H 101 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR H 101 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR H 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 101 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 375 " -0.034 2.00e-02 2.50e+03 2.75e-02 1.33e+01 pdb=" CG PHE N 375 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE N 375 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE N 375 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE N 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 375 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE N 375 " -0.007 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 1 2.04 - 2.75: 2988 2.75 - 3.47: 34904 3.47 - 4.18: 59806 4.18 - 4.90: 97644 Nonbonded interactions: 195343 Sorted by model distance: nonbonded pdb="MG MG E 101 " pdb="MG MG E 102 " model vdw 1.323 1.300 nonbonded pdb=" O2' A E 65 " pdb="MG MG E 102 " model vdw 2.108 2.170 nonbonded pdb=" N3 A E 65 " pdb="MG MG E 102 " model vdw 2.206 2.250 nonbonded pdb=" O2' A E 36 " pdb=" OH TYR H 83 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 112 " pdb=" OG1 THR A 138 " model vdw 2.218 3.040 ... (remaining 195338 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 'D' and (resid 38 through 114 or (resid 115 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 or (resid 119 through 123 a \ nd (name N or name CA or name C or name O or name CB )) or resid 124 or (resid 1 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 126 through \ 427)) selection = (chain 'H' and (resid 38 through 197 or (resid 198 through 219 and (name N or na \ me CA or name C or name O or name CB )) or resid 220 through 294 or (resid 295 t \ hrough 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 427)) } ncs_group { reference = (chain 'N' and ((resid 226 through 229 and (name N or name CA or name C or name \ O or name CB )) or resid 230 through 255 or (resid 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 through 264 or (resid 265 and (name \ N or name CA or name C or name O or name CB )) or resid 266 through 267 or (res \ id 268 through 269 and (name N or name CA or name C or name O or name CB )) or r \ esid 270 through 281 or (resid 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 289 or (resid 290 and (name N or name CA or nam \ e C or name O or name CB )) or resid 291 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 325 or (resid 326 and (name N or name CA or name C or name O or nam \ e CB )) or resid 327 through 330 or (resid 331 through 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 349 or (resid 350 and ( \ name N or name CA or name C or name O or name CB )) or resid 351 through 355 or \ (resid 356 and (name N or name CA or name C or name O or name CB )) or resid 357 \ through 361 or (resid 362 and (name N or name CA or name C or name O or name CB \ )) or resid 363 through 367 or (resid 369 through 371 and (name N or name CA or \ name C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name \ N or name CA or name C or name O or name CB )) or resid 382 through 396 or (res \ id 397 and (name N or name CA or name C or name O or name CB )) or resid 398 thr \ ough 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) \ or resid 421 through 429 or (resid 430 through 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 440 or (resid 441 through 442 a \ nd (name N or name CA or name C or name O or name CB )) or resid 443 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 or (resid 450 through 453 and (name N or name CA or name C or name O or nam \ e CB )) or resid 467 through 468 or (resid 469 and (name N or name CA or name C \ or name O or name CB )) or resid 470 or (resid 471 and (name N or name CA or nam \ e C or name O or name CB )) or resid 472 or (resid 473 through 474 and (name N o \ r name CA or name C or name O or name CB )) or resid 475 through 484 or (resid 4 \ 85 through 486 and (name N or name CA or name C or name O or name CB )) or resid \ 487 through 502 or (resid 503 and (name N or name CA or name C or name O or nam \ e CB )) or resid 504 through 509 or (resid 510 and (name N or name CA or name C \ or name O or name CB )) or resid 511 through 520 or (resid 521 and (name N or na \ me CA or name C or name O or name CB )) or resid 522 through 536 or (resid 537 a \ nd (name N or name CA or name C or name O or name CB )) or resid 538 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 595 or (resid 596 through 598 and (name N or name CA or name C or n \ ame O or name CB )) or resid 599 through 605 or (resid 606 and (name N or name C \ A or name C or name O or name CB )) or resid 607 through 644 or (resid 645 and ( \ name N or name CA or name C or name O or name CB )) or resid 646 through 650 or \ (resid 651 and (name N or name CA or name C or name O or name CB )) or resid 652 \ through 664 or resid 666 through 671 or (resid 672 and (name N or name CA or na \ me C or name O or name CB )) or resid 673 through 679)) selection = (chain 'O' and (resid 226 through 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or (resid 251 through 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 or (resid 258 and (name N or name C \ A or name C or name O or name CB )) or resid 259 through 260 or (resid 261 and ( \ name N or name CA or name C or name O or name CB )) or resid 262 or (resid 263 a \ nd (name N or name CA or name C or name O or name CB )) or resid 264 through 270 \ or (resid 271 through 272 and (name N or name CA or name C or name O or name CB \ )) or resid 273 through 275 or (resid 276 through 277 and (name N or name CA or \ name C or name O or name CB )) or resid 278 through 283 or (resid 284 and (name \ N or name CA or name C or name O or name CB )) or resid 285 or (resid 286 throu \ gh 287 and (name N or name CA or name C or name O or name CB )) or resid 288 thr \ ough 297 or (resid 298 through 301 and (name N or name CA or name C or name O or \ name CB )) or (resid 307 through 308 and (name N or name CA or name C or name O \ or name CB )) or (resid 309 and (name N or name CA or name C or name O or name \ CB or name OG1)) or (resid 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 329 or (resid 330 through 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 334 or (resid 335 and ( \ name N or name CA or name C or name O or name CB )) or resid 336 through 340 or \ (resid 341 through 342 and (name N or name CA or name C or name O or name CB )) \ or resid 343 through 348 or (resid 349 through 350 and (name N or name CA or nam \ e C or name O or name CB )) or resid 351 through 364 or (resid 365 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 366 through 367 \ or resid 369 through 383 or (resid 384 and (name N or name CA or name C or name \ O or name CB )) or resid 385 through 389 or (resid 390 and (name N or name CA or \ name C or name O or name CB )) or resid 391 through 393 or (resid 394 through 3 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 396 through \ 427 or (resid 428 and (name N or name CA or name C or name O or name CB )) or r \ esid 429 through 441 or (resid 442 and (name N or name CA or name C or name O or \ name CB )) or resid 443 through 485 or (resid 486 and (name N or name CA or nam \ e C or name O or name CB )) or resid 487 through 489 or (resid 490 through 493 a \ nd (name N or name CA or name C or name O or name CB )) or resid 494 through 496 \ or (resid 497 through 498 and (name N or name CA or name C or name O or name CB \ )) or resid 499 through 505 or (resid 506 through 507 and (name N or name CA or \ name C or name O or name CB )) or resid 508 through 511 or (resid 512 and (name \ N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 throu \ gh 515 and (name N or name CA or name C or name O or name CB )) or resid 516 thr \ ough 517 or (resid 518 and (name N or name CA or name C or name O or name CB or \ name CG1)) or resid 519 or (resid 520 through 521 and (name N or name CA or name \ C or name O or name CB )) or resid 522 through 523 or (resid 524 through 525 an \ d (name N or name CA or name C or name O or name CB )) or resid 526 through 531 \ or (resid 532 and (name N or name CA or name C or name O or name CB )) or resid \ 533 through 549 or (resid 550 and (name N or name CA or name C or name O or name \ CB )) or resid 551 through 620 or (resid 621 through 623 and (name N or name CA \ or name C or name O or name CB )) or resid 624 or (resid 625 and (name N or nam \ e CA or name C or name O or name CB )) or resid 626 through 654 or (resid 655 th \ rough 656 and (name N or name CA or name C or name O or name CB )) or resid 657 \ through 664 or resid 666 through 679)) } 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=0.00 max=1.00 mean=0.99 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24149 Z= 0.261 Angle : 1.167 16.795 33098 Z= 0.621 Chirality : 0.079 0.442 3762 Planarity : 0.007 0.078 4040 Dihedral : 15.916 179.492 8844 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.05 % Favored : 84.84 % Rotamer: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.65 % 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: -4.78 (0.13), residues: 2837 helix: -2.71 (0.13), residues: 852 sheet: -3.10 (0.28), residues: 261 loop : -3.62 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 293 TYR 0.068 0.003 TYR H 101 PHE 0.062 0.004 PHE N 375 TRP 0.023 0.003 TRP O 600 HIS 0.015 0.002 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.26 (24149) covalent geometry : angle 1.16705 / 0.62 (33098) hydrogen bonds : bond 0.13077 / 8.68 ( 806) hydrogen bonds : angle 8.51974 / 5.73 ( 2301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.880 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: A 238 MET cc_start: 0.7472 (mtp) cc_final: 0.7198 (mpp) REVERT: A 265 LEU cc_start: 0.9537 (tt) cc_final: 0.9336 (tt) REVERT: A 618 MET cc_start: 0.8874 (mtp) cc_final: 0.8622 (ttm) REVERT: A 703 MET cc_start: 0.9443 (mmt) cc_final: 0.9116 (mmm) REVERT: A 738 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8758 (mm-30) REVERT: A 835 GLU cc_start: 0.9544 (tt0) cc_final: 0.9286 (pm20) REVERT: A 1006 MET cc_start: 0.9564 (ttt) cc_final: 0.9278 (ttt) REVERT: N 649 MET cc_start: 0.8616 (ttm) cc_final: 0.8327 (tpt) REVERT: O 628 MET cc_start: 0.8304 (tpp) cc_final: 0.7580 (ttp) REVERT: O 649 MET cc_start: 0.7807 (ttm) cc_final: 0.7454 (tmm) outliers start: 4 outliers final: 0 residues processed: 167 average time/residue: 0.1876 time to fit residues: 48.0893 Evaluate side-chains 92 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 210 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 454 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A 748 ASN A1025 ASN A1027 ASN D 85 ASN D 269 HIS ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN H 139 ASN H 234 GLN H 285 ASN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 GLN ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 ASN N 391 ASN N 399 ASN N 445 HIS N 583 ASN N 632 HIS N 638 ASN O 270 ASN O 293 ASN O 489 ASN O 559 GLN O 575 ASN O 583 ASN O 618 HIS O 619 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.039196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.027267 restraints weight = 409319.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.027914 restraints weight = 312893.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.028431 restraints weight = 255361.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.028832 restraints weight = 217029.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.029141 restraints weight = 190826.484| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24149 Z= 0.242 Angle : 1.026 17.313 33098 Z= 0.499 Chirality : 0.092 2.771 3762 Planarity : 0.005 0.067 4040 Dihedral : 16.303 164.107 3888 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.04 % Favored : 86.92 % Rotamer: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.02 (0.14), residues: 2837 helix: -1.45 (0.15), residues: 892 sheet: -3.06 (0.26), residues: 303 loop : -3.46 (0.13), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 68 TYR 0.038 0.002 TYR H 101 PHE 0.024 0.002 PHE N 547 TRP 0.022 0.002 TRP A 324 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (24149) covalent geometry : angle 1.02575 / 0.50 (33098) hydrogen bonds : bond 0.04927 / 3.27 ( 806) hydrogen bonds : angle 6.91949 / 4.72 ( 2301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.910 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: A 265 LEU cc_start: 0.8275 (tt) cc_final: 0.7718 (tt) REVERT: A 1006 MET cc_start: 0.9370 (ttt) cc_final: 0.9112 (ptm) REVERT: F 175 GLU cc_start: 0.8945 (tp30) cc_final: 0.8742 (pm20) REVERT: O 297 LEU cc_start: 0.8862 (tt) cc_final: 0.8507 (mt) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.1892 time to fit residues: 33.5660 Evaluate side-chains 87 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 129 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 245 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A1025 ASN D 302 HIS ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 ASN ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.039318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.027404 restraints weight = 402987.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.028145 restraints weight = 298820.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.028706 restraints weight = 238346.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.029102 restraints weight = 199865.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.029451 restraints weight = 175446.092| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24149 Z= 0.169 Angle : 0.823 10.949 33098 Z= 0.407 Chirality : 0.061 0.653 3762 Planarity : 0.004 0.065 4040 Dihedral : 16.041 173.353 3888 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.40 (0.14), residues: 2837 helix: -0.69 (0.16), residues: 893 sheet: -2.62 (0.29), residues: 278 loop : -3.27 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 68 TYR 0.026 0.002 TYR H 101 PHE 0.017 0.002 PHE O 357 TRP 0.019 0.002 TRP A 324 HIS 0.005 0.001 HIS N 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (24149) covalent geometry : angle 0.82251 / 0.41 (33098) hydrogen bonds : bond 0.04115 / 2.75 ( 806) hydrogen bonds : angle 6.37887 / 4.35 ( 2301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.877 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: A 265 LEU cc_start: 0.8385 (tt) cc_final: 0.7893 (tt) REVERT: A 1006 MET cc_start: 0.9374 (ttt) cc_final: 0.9090 (ptm) REVERT: F 112 MET cc_start: 0.8070 (pmm) cc_final: 0.7865 (pmm) REVERT: H 112 MET cc_start: 0.7776 (mtm) cc_final: 0.7317 (ptp) REVERT: N 551 MET cc_start: 0.5764 (pmm) cc_final: 0.5332 (pmm) REVERT: O 297 LEU cc_start: 0.8720 (tt) cc_final: 0.8352 (mt) REVERT: O 564 TYR cc_start: 0.7957 (p90) cc_final: 0.7714 (p90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1696 time to fit residues: 30.9588 Evaluate side-chains 90 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 88 optimal weight: 5.9990 chunk 181 optimal weight: 50.0000 chunk 130 optimal weight: 40.0000 chunk 269 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS A1025 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 ASN ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.038773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.027021 restraints weight = 410208.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.027669 restraints weight = 313431.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.028172 restraints weight = 255052.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.028562 restraints weight = 216740.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.028878 restraints weight = 190480.391| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 115 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24149 Z= 0.206 Angle : 0.827 10.997 33098 Z= 0.414 Chirality : 0.057 0.509 3762 Planarity : 0.004 0.064 4040 Dihedral : 15.982 177.411 3888 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.24 (0.15), residues: 2837 helix: -0.50 (0.17), residues: 890 sheet: -2.63 (0.29), residues: 276 loop : -3.19 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 312 TYR 0.034 0.002 TYR H 101 PHE 0.031 0.002 PHE F 168 TRP 0.020 0.002 TRP O 403 HIS 0.006 0.002 HIS N 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (24149) covalent geometry : angle 0.82652 / 0.41 (33098) hydrogen bonds : bond 0.04357 / 2.94 ( 806) hydrogen bonds : angle 6.43977 / 4.42 ( 2301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.923 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: A 236 ARG cc_start: 0.5029 (mpt90) cc_final: 0.4570 (mmt90) REVERT: A 265 LEU cc_start: 0.8240 (tt) cc_final: 0.7730 (tt) REVERT: A 1006 MET cc_start: 0.9362 (ttt) cc_final: 0.9087 (ptm) REVERT: F 87 ASN cc_start: 0.8088 (t0) cc_final: 0.7639 (m-40) REVERT: N 638 ASN cc_start: 0.8764 (m110) cc_final: 0.8323 (t0) REVERT: O 551 MET cc_start: 0.7064 (tmm) cc_final: 0.6793 (tmm) REVERT: O 564 TYR cc_start: 0.7855 (p90) cc_final: 0.7634 (p90) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1612 time to fit residues: 27.5742 Evaluate side-chains 83 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 141 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 559 GLN ** O 559 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 = 0.3380 r_free = 0.3380 target = 0.038487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.026799 restraints weight = 413595.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.027461 restraints weight = 312702.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.027965 restraints weight = 253056.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.028362 restraints weight = 214364.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.028675 restraints weight = 187749.321| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 115 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 115 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24149 Z= 0.202 Angle : 0.812 12.181 33098 Z= 0.407 Chirality : 0.055 0.484 3762 Planarity : 0.004 0.060 4040 Dihedral : 15.976 178.672 3888 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.08 (0.15), residues: 2837 helix: -0.36 (0.17), residues: 882 sheet: -2.51 (0.30), residues: 266 loop : -3.08 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 403 TYR 0.035 0.002 TYR H 101 PHE 0.020 0.002 PHE A1091 TRP 0.018 0.002 TRP N 346 HIS 0.009 0.002 HIS O 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (24149) covalent geometry : angle 0.81242 / 0.41 (33098) hydrogen bonds : bond 0.04254 / 2.87 ( 806) hydrogen bonds : angle 6.44316 / 4.41 ( 2301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.940 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: A 265 LEU cc_start: 0.8268 (tt) cc_final: 0.7811 (tt) REVERT: A 438 MET cc_start: 0.6913 (tpt) cc_final: 0.6692 (tpt) REVERT: A 808 TYR cc_start: 0.9146 (m-80) cc_final: 0.8637 (m-80) REVERT: A 1006 MET cc_start: 0.9332 (ttt) cc_final: 0.9064 (ptm) REVERT: N 551 MET cc_start: 0.5822 (pmm) cc_final: 0.5362 (pmm) REVERT: O 648 LEU cc_start: 0.8906 (tp) cc_final: 0.8579 (pt) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1807 time to fit residues: 30.8420 Evaluate side-chains 78 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 229 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 262 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 102 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 205 optimal weight: 0.4980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.039362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.027299 restraints weight = 407519.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.027995 restraints weight = 306610.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.028531 restraints weight = 246812.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.028946 restraints weight = 208126.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.029275 restraints weight = 181906.036| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24149 Z= 0.149 Angle : 0.753 12.607 33098 Z= 0.374 Chirality : 0.054 0.434 3762 Planarity : 0.004 0.057 4040 Dihedral : 15.820 179.619 3888 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.80 (0.15), residues: 2837 helix: 0.02 (0.17), residues: 886 sheet: -2.35 (0.30), residues: 271 loop : -3.00 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1045 TYR 0.040 0.002 TYR H 101 PHE 0.035 0.002 PHE F 168 TRP 0.019 0.002 TRP N 346 HIS 0.005 0.001 HIS N 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (24149) covalent geometry : angle 0.75260 / 0.37 (33098) hydrogen bonds : bond 0.03767 / 2.54 ( 806) hydrogen bonds : angle 6.11256 / 4.20 ( 2301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.830 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 265 LEU cc_start: 0.8291 (tt) cc_final: 0.7875 (tt) REVERT: A 1006 MET cc_start: 0.9314 (ttt) cc_final: 0.9059 (ptm) REVERT: N 551 MET cc_start: 0.5605 (pmm) cc_final: 0.5122 (pmm) REVERT: O 551 MET cc_start: 0.7014 (tmm) cc_final: 0.6617 (tmm) REVERT: O 564 TYR cc_start: 0.7875 (p90) cc_final: 0.7654 (p90) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.1561 time to fit residues: 28.1501 Evaluate side-chains 84 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 105 optimal weight: 0.9990 chunk 214 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 19 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 619 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.039508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.027435 restraints weight = 403497.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.028127 restraints weight = 303252.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.028678 restraints weight = 244717.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.029086 restraints weight = 206205.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.029416 restraints weight = 180417.263| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24149 Z= 0.142 Angle : 0.732 12.305 33098 Z= 0.363 Chirality : 0.053 0.388 3762 Planarity : 0.004 0.056 4040 Dihedral : 15.744 178.171 3888 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.62 (0.15), residues: 2837 helix: 0.22 (0.17), residues: 892 sheet: -2.16 (0.31), residues: 254 loop : -2.96 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1045 TYR 0.038 0.002 TYR H 101 PHE 0.017 0.001 PHE D 86 TRP 0.019 0.002 TRP N 346 HIS 0.007 0.001 HIS O 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (24149) covalent geometry : angle 0.73155 / 0.36 (33098) hydrogen bonds : bond 0.03614 / 2.42 ( 806) hydrogen bonds : angle 5.95014 / 4.08 ( 2301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.962 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: A 265 LEU cc_start: 0.8414 (tt) cc_final: 0.8010 (tt) REVERT: A 1006 MET cc_start: 0.9275 (ttt) cc_final: 0.9008 (ptm) REVERT: F 87 ASN cc_start: 0.8256 (t0) cc_final: 0.7989 (m-40) REVERT: N 551 MET cc_start: 0.5606 (pmm) cc_final: 0.5105 (pmm) REVERT: N 638 ASN cc_start: 0.8395 (m110) cc_final: 0.7933 (t0) REVERT: N 649 MET cc_start: 0.7777 (tpt) cc_final: 0.7527 (tpt) REVERT: O 551 MET cc_start: 0.7002 (tmm) cc_final: 0.6591 (tmm) REVERT: O 564 TYR cc_start: 0.7865 (p90) cc_final: 0.7644 (p90) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1633 time to fit residues: 29.4377 Evaluate side-chains 79 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 246 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 232 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN N 316 ASN ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.038048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.026473 restraints weight = 417739.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.027097 restraints weight = 318145.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027575 restraints weight = 259406.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.027946 restraints weight = 221039.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.028246 restraints weight = 194559.859| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24149 Z= 0.230 Angle : 0.839 12.070 33098 Z= 0.421 Chirality : 0.055 0.412 3762 Planarity : 0.005 0.056 4040 Dihedral : 16.025 177.288 3888 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 27.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.35 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.84 (0.15), residues: 2837 helix: -0.20 (0.17), residues: 889 sheet: -2.09 (0.31), residues: 249 loop : -2.97 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 403 TYR 0.034 0.002 TYR H 101 PHE 0.029 0.002 PHE N 375 TRP 0.021 0.003 TRP A 45 HIS 0.009 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (24149) covalent geometry : angle 0.83899 / 0.42 (33098) hydrogen bonds : bond 0.04409 / 2.98 ( 806) hydrogen bonds : angle 6.43660 / 4.42 ( 2301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.890 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: A 265 LEU cc_start: 0.8329 (tt) cc_final: 0.7918 (tt) REVERT: A 370 MET cc_start: 0.5104 (ppp) cc_final: 0.4776 (ppp) REVERT: A 1006 MET cc_start: 0.9144 (ttt) cc_final: 0.8919 (ptm) REVERT: F 87 ASN cc_start: 0.8023 (t0) cc_final: 0.7683 (m-40) REVERT: F 112 MET cc_start: 0.7999 (pmm) cc_final: 0.7707 (pmm) REVERT: N 551 MET cc_start: 0.5829 (pmm) cc_final: 0.5313 (pmm) REVERT: O 551 MET cc_start: 0.7160 (tmm) cc_final: 0.6595 (tmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1689 time to fit residues: 27.1244 Evaluate side-chains 77 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 218 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.038829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.026966 restraints weight = 408773.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.027664 restraints weight = 306275.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.028188 restraints weight = 245923.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.028612 restraints weight = 207242.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.028928 restraints weight = 180699.841| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24149 Z= 0.160 Angle : 0.762 12.311 33098 Z= 0.378 Chirality : 0.054 0.377 3762 Planarity : 0.004 0.055 4040 Dihedral : 15.875 177.211 3888 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.66 (0.15), residues: 2837 helix: 0.07 (0.17), residues: 894 sheet: -2.07 (0.31), residues: 261 loop : -2.92 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 110 TYR 0.032 0.002 TYR H 101 PHE 0.019 0.002 PHE N 375 TRP 0.019 0.002 TRP N 346 HIS 0.007 0.001 HIS O 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (24149) covalent geometry : angle 0.76208 / 0.38 (33098) hydrogen bonds : bond 0.03818 / 2.55 ( 806) hydrogen bonds : angle 6.16805 / 4.22 ( 2301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.911 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: A 265 LEU cc_start: 0.8423 (tt) cc_final: 0.8036 (tt) REVERT: A 370 MET cc_start: 0.4321 (ppp) cc_final: 0.4029 (ppp) REVERT: F 87 ASN cc_start: 0.8186 (t0) cc_final: 0.7932 (m-40) REVERT: N 551 MET cc_start: 0.5738 (pmm) cc_final: 0.5206 (pmm) REVERT: O 551 MET cc_start: 0.7078 (tmm) cc_final: 0.6511 (tmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1680 time to fit residues: 26.8968 Evaluate side-chains 75 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 237 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.039058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.027116 restraints weight = 406431.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.027827 restraints weight = 304740.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.028356 restraints weight = 244345.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.028778 restraints weight = 206058.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.029108 restraints weight = 179599.039| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24149 Z= 0.150 Angle : 0.746 11.724 33098 Z= 0.370 Chirality : 0.053 0.363 3762 Planarity : 0.004 0.056 4040 Dihedral : 15.777 176.422 3888 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.57 (0.15), residues: 2837 helix: 0.16 (0.17), residues: 900 sheet: -2.01 (0.31), residues: 264 loop : -2.90 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 149 TYR 0.045 0.002 TYR H 101 PHE 0.018 0.002 PHE N 612 TRP 0.019 0.002 TRP N 346 HIS 0.007 0.001 HIS O 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (24149) covalent geometry : angle 0.74575 / 0.37 (33098) hydrogen bonds : bond 0.03681 / 2.47 ( 806) hydrogen bonds : angle 6.09246 / 4.17 ( 2301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.910 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: A 265 LEU cc_start: 0.8432 (tt) cc_final: 0.8063 (tt) REVERT: A 370 MET cc_start: 0.4180 (ppp) cc_final: 0.3936 (ppp) REVERT: N 551 MET cc_start: 0.5527 (pmm) cc_final: 0.5010 (pmm) REVERT: N 638 ASN cc_start: 0.8502 (m110) cc_final: 0.8119 (t0) REVERT: O 551 MET cc_start: 0.7056 (tmm) cc_final: 0.6613 (tmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1601 time to fit residues: 25.4359 Evaluate side-chains 77 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 289 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 chunk 208 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.038858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.026991 restraints weight = 408107.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027687 restraints weight = 306518.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.028223 restraints weight = 246476.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.028632 restraints weight = 207816.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.028943 restraints weight = 181439.875| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24149 Z= 0.161 Angle : 0.753 11.471 33098 Z= 0.375 Chirality : 0.053 0.359 3762 Planarity : 0.004 0.055 4040 Dihedral : 15.737 175.854 3888 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.57 (0.15), residues: 2837 helix: 0.16 (0.17), residues: 901 sheet: -2.01 (0.31), residues: 263 loop : -2.89 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 149 TYR 0.047 0.002 TYR H 101 PHE 0.018 0.002 PHE N 375 TRP 0.018 0.002 TRP N 346 HIS 0.007 0.001 HIS O 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (24149) covalent geometry : angle 0.75348 / 0.38 (33098) hydrogen bonds : bond 0.03742 / 2.50 ( 806) hydrogen bonds : angle 6.08834 / 4.16 ( 2301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5344.83 seconds wall clock time: 93 minutes 10.30 seconds (5590.30 seconds total)