Starting phenix.real_space_refine on Fri Mar 6 02:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r5k_4728/03_2026/6r5k_4728.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r5k_4728/03_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_4728/03_2026/6r5k_4728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r5k_4728/03_2026/6r5k_4728.map" model { file = "/net/cci-nas-00/data/ceres_data/6r5k_4728/03_2026/6r5k_4728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r5k_4728/03_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-dev-5986/lib/python3.9/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: {'RNA': 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: 5.36, per 1000 atoms: 0.23 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: 1.54 Conformation dependent library (CDL) restraints added in 1.1 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: 3.22 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: 4.39 Time building geometry restraints manager: 2.03 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: 32488 3.36 - 6.72: 523 6.72 - 10.08: 76 10.08 - 13.44: 9 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: 14053 35.90 - 71.80: 201 71.80 - 107.70: 17 107.70 - 143.59: 4 143.59 - 179.49: 3 Dihedral angle restraints: 14278 sinusoidal: 5860 harmonic: 8418 Sorted by residual: dihedral pdb=" CA PRO A 58 " pdb=" C PRO A 58 " pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" C5' A E 49 " pdb=" C4' A E 49 " pdb=" C3' A E 49 " pdb=" O3' A E 49 " ideal model delta sinusoidal sigma weight residual 147.00 80.16 66.84 1 8.00e+00 1.56e-02 9.10e+01 dihedral pdb=" C4' A E 49 " pdb=" C3' A E 49 " pdb=" C2' A E 49 " pdb=" C1' A E 49 " ideal model delta sinusoidal sigma weight residual -35.00 31.51 -66.51 1 8.00e+00 1.56e-02 9.02e+01 ... (remaining 14275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3105 0.078 - 0.155: 564 0.155 - 0.233: 78 0.233 - 0.311: 12 0.311 - 0.389: 3 Chirality restraints: 3762 Sorted by residual: 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 chirality pdb=" CB ILE A 109 " pdb=" CA ILE A 109 " pdb=" CG1 ILE A 109 " pdb=" CG2 ILE A 109 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' A E 7 " pdb=" C4' A E 7 " pdb=" O3' A E 7 " pdb=" C2' A E 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.44e+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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.560 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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= 0.257 Angle : 1.110 16.795 33098 Z= 0.602 Chirality : 0.061 0.389 3762 Planarity : 0.007 0.078 4040 Dihedral : 13.737 179.492 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 covalent geometry : bond 0.00528 (24149) covalent geometry : angle 1.10955 (33098) hydrogen bonds : bond 0.13077 ( 806) hydrogen bonds : angle 8.51974 ( 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 : 0.876 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: 0.1865 time to fit residues: 47.4013 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 : 0.758 ------------------------------------------------------------------------------- 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: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3418 r_free = 0.3418 target = 0.039424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.027373 restraints weight = 407118.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.028048 restraints weight = 309771.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.028576 restraints weight = 251593.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.028981 restraints weight = 213512.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.029288 restraints weight = 187500.675| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 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 = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24149 Z= 0.196 Angle : 0.754 11.162 33098 Z= 0.399 Chirality : 0.045 0.231 3762 Planarity : 0.005 0.065 4040 Dihedral : 14.260 177.180 3888 Min Nonbonded Distance : 1.214 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.72 % Favored : 87.24 % Rotamer: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.92 (0.14), residues: 2837 helix: -1.35 (0.15), residues: 888 sheet: -3.01 (0.27), residues: 293 loop : -3.42 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 571 TYR 0.039 0.002 TYR H 101 PHE 0.024 0.002 PHE N 375 TRP 0.022 0.002 TRP A 324 HIS 0.006 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00395 (24149) covalent geometry : angle 0.75351 (33098) hydrogen bonds : bond 0.04684 ( 806) hydrogen bonds : angle 6.79342 ( 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 119 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.862 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: 0.8206 (tt) cc_final: 0.7657 (tt) REVERT: A 1006 MET cc_start: 0.9360 (ttt) cc_final: 0.9104 (ptm) REVERT: O 297 LEU cc_start: 0.8763 (tt) cc_final: 0.8398 (mt) REVERT: O 564 TYR cc_start: 0.8127 (p90) cc_final: 0.7916 (p90) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.1882 time to fit residues: 33.8917 Evaluate side-chains 87 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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: 50.0000 chunk 21 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 247 optimal weight: 30.0000 chunk 245 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A1025 ASN 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.039091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.027192 restraints weight = 406231.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.027934 restraints weight = 300758.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.028489 restraints weight = 239503.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.028911 restraints weight = 200781.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.029246 restraints weight = 174844.223| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 116 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24149 Z= 0.164 Angle : 0.697 10.527 33098 Z= 0.366 Chirality : 0.045 0.217 3762 Planarity : 0.004 0.065 4040 Dihedral : 13.960 179.828 3888 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -0.68 (0.16), residues: 895 sheet: -2.56 (0.29), residues: 288 loop : -3.29 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 93 TYR 0.025 0.002 TYR O 564 PHE 0.016 0.002 PHE O 357 TRP 0.019 0.002 TRP A 324 HIS 0.006 0.001 HIS A1066 Details of bonding type rmsd covalent geometry : bond 0.00331 (24149) covalent geometry : angle 0.69662 (33098) hydrogen bonds : bond 0.04198 ( 806) hydrogen bonds : angle 6.42411 ( 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 110 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.896 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: 0.8290 (tt) cc_final: 0.7783 (tt) REVERT: A 1006 MET cc_start: 0.9383 (ttt) cc_final: 0.9091 (ptm) REVERT: F 112 MET cc_start: 0.8027 (pmm) cc_final: 0.7818 (pmm) REVERT: N 551 MET cc_start: 0.5771 (pmm) cc_final: 0.5337 (pmm) REVERT: O 564 TYR cc_start: 0.7926 (p90) cc_final: 0.7678 (p90) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1668 time to fit residues: 28.9819 Evaluate side-chains 88 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 8.9990 chunk 181 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 269 optimal weight: 1.9990 chunk 225 optimal weight: 0.0870 chunk 49 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 178 optimal weight: 30.0000 overall best weight: 4.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** 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 328 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 = 0.3408 r_free = 0.3408 target = 0.039216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.027253 restraints weight = 406706.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.027997 restraints weight = 301057.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.028551 restraints weight = 239662.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.028976 restraints weight = 200950.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.029302 restraints weight = 175078.908| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 116 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 116 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2853 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= 0.155 Angle : 0.670 9.886 33098 Z= 0.350 Chirality : 0.044 0.188 3762 Planarity : 0.004 0.063 4040 Dihedral : 13.762 179.906 3888 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -3.11 (0.15), residues: 2837 helix: -0.30 (0.17), residues: 894 sheet: -2.58 (0.29), residues: 286 loop : -3.16 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 403 TYR 0.029 0.002 TYR H 101 PHE 0.014 0.002 PHE O 357 TRP 0.017 0.002 TRP N 346 HIS 0.006 0.001 HIS A1066 Details of bonding type rmsd covalent geometry : bond 0.00316 (24149) covalent geometry : angle 0.66977 (33098) hydrogen bonds : bond 0.03963 ( 806) hydrogen bonds : angle 6.22779 ( 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 110 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.771 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: A 265 LEU cc_start: 0.8262 (tt) cc_final: 0.7756 (tt) REVERT: A 1006 MET cc_start: 0.9415 (ttt) cc_final: 0.9146 (ptm) REVERT: N 551 MET cc_start: 0.5505 (pmm) cc_final: 0.5090 (pmm) REVERT: N 638 ASN cc_start: 0.8729 (m110) cc_final: 0.8484 (m-40) REVERT: O 551 MET cc_start: 0.6933 (tmm) cc_final: 0.6701 (tmm) REVERT: O 648 LEU cc_start: 0.9047 (tp) cc_final: 0.8743 (pt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1636 time to fit residues: 28.7463 Evaluate side-chains 84 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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: 0.9990 chunk 110 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 39 optimal weight: 0.0770 chunk 12 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 282 optimal weight: 0.0170 overall best weight: 3.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN D 302 HIS ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN F 89 HIS ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 679 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.039682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.027562 restraints weight = 401506.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.028318 restraints weight = 295703.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.028902 restraints weight = 234667.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.029341 restraints weight = 196310.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.029673 restraints weight = 170693.520| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24149 Z= 0.129 Angle : 0.632 9.511 33098 Z= 0.331 Chirality : 0.043 0.234 3762 Planarity : 0.004 0.059 4040 Dihedral : 13.562 178.775 3888 Min Nonbonded Distance : 1.481 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -2.79 (0.15), residues: 2837 helix: 0.08 (0.17), residues: 891 sheet: -2.39 (0.29), residues: 290 loop : -3.03 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 239 TYR 0.033 0.002 TYR H 101 PHE 0.033 0.001 PHE F 168 TRP 0.017 0.002 TRP N 346 HIS 0.006 0.001 HIS A1066 Details of bonding type rmsd covalent geometry : bond 0.00267 (24149) covalent geometry : angle 0.63193 (33098) hydrogen bonds : bond 0.03635 ( 806) hydrogen bonds : angle 5.99395 ( 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 115 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8322 (tt) cc_final: 0.7811 (tt) REVERT: A 1006 MET cc_start: 0.9384 (ttt) cc_final: 0.9090 (ptm) REVERT: N 551 MET cc_start: 0.5725 (pmm) cc_final: 0.5238 (pmm) REVERT: O 449 MET cc_start: 0.8979 (mtt) cc_final: 0.8703 (mpp) REVERT: O 551 MET cc_start: 0.6821 (tmm) cc_final: 0.6619 (tmm) REVERT: O 564 TYR cc_start: 0.7938 (p90) cc_final: 0.7706 (p90) REVERT: O 648 LEU cc_start: 0.9013 (tp) cc_final: 0.8738 (pt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1681 time to fit residues: 30.3958 Evaluate side-chains 85 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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: 9.9990 chunk 147 optimal weight: 40.0000 chunk 262 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 205 optimal weight: 0.0870 overall best weight: 4.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 ASN N 679 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.039249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.027182 restraints weight = 411455.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.027890 restraints weight = 308480.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.028423 restraints weight = 247451.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.028850 restraints weight = 208678.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.029176 restraints weight = 182258.187| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24149 Z= 0.160 Angle : 0.664 9.564 33098 Z= 0.346 Chirality : 0.044 0.226 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.577 177.310 3888 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -2.71 (0.15), residues: 2837 helix: 0.13 (0.17), residues: 888 sheet: -2.42 (0.28), residues: 301 loop : -2.95 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 358 TYR 0.039 0.002 TYR H 101 PHE 0.016 0.002 PHE O 392 TRP 0.017 0.002 TRP N 346 HIS 0.006 0.001 HIS A1066 Details of bonding type rmsd covalent geometry : bond 0.00327 (24149) covalent geometry : angle 0.66418 (33098) hydrogen bonds : bond 0.03813 ( 806) hydrogen bonds : angle 6.05965 ( 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 107 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.863 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: A 265 LEU cc_start: 0.8262 (tt) cc_final: 0.7797 (tt) REVERT: A 1006 MET cc_start: 0.9350 (ttt) cc_final: 0.9079 (ptm) REVERT: A 1019 ASN cc_start: 0.9443 (t0) cc_final: 0.9111 (t0) REVERT: N 551 MET cc_start: 0.5579 (pmm) cc_final: 0.5129 (pmm) REVERT: N 638 ASN cc_start: 0.8477 (m110) cc_final: 0.7996 (t0) REVERT: O 449 MET cc_start: 0.8917 (mtt) cc_final: 0.8584 (mpp) REVERT: O 551 MET cc_start: 0.7049 (tmm) cc_final: 0.6567 (tmm) REVERT: O 564 TYR cc_start: 0.7865 (p90) cc_final: 0.7652 (p90) REVERT: O 648 LEU cc_start: 0.9036 (tp) cc_final: 0.8764 (pt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1514 time to fit residues: 26.2393 Evaluate side-chains 81 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 9.9990 chunk 214 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN A1084 HIS D 406 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 ASN ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 559 GLN N 679 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.038480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.026682 restraints weight = 414633.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.027356 restraints weight = 312442.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.027867 restraints weight = 251817.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.028261 restraints weight = 213015.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.028570 restraints weight = 186785.513| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3847 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= 0.198 Angle : 0.714 10.856 33098 Z= 0.373 Chirality : 0.045 0.261 3762 Planarity : 0.004 0.055 4040 Dihedral : 13.704 174.143 3888 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 0.04 % Allowed : 2.14 % Favored : 97.81 % 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: -2.71 (0.15), residues: 2837 helix: 0.08 (0.17), residues: 884 sheet: -2.09 (0.31), residues: 262 loop : -2.99 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 358 TYR 0.038 0.002 TYR H 101 PHE 0.018 0.002 PHE A1091 TRP 0.018 0.002 TRP N 346 HIS 0.013 0.002 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00402 (24149) covalent geometry : angle 0.71440 (33098) hydrogen bonds : bond 0.04180 ( 806) hydrogen bonds : angle 6.33200 ( 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 100 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.826 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: A 265 LEU cc_start: 0.8274 (tt) cc_final: 0.7798 (tt) REVERT: A 1006 MET cc_start: 0.9306 (ttt) cc_final: 0.9035 (ptm) REVERT: F 112 MET cc_start: 0.7752 (pmm) cc_final: 0.7489 (pmm) REVERT: N 551 MET cc_start: 0.5764 (pmm) cc_final: 0.5259 (pmm) REVERT: O 449 MET cc_start: 0.8958 (mtt) cc_final: 0.8721 (mpp) REVERT: O 551 MET cc_start: 0.6971 (tmm) cc_final: 0.6707 (tmm) REVERT: O 564 TYR cc_start: 0.7839 (p90) cc_final: 0.7637 (p90) REVERT: O 648 LEU cc_start: 0.9112 (tp) cc_final: 0.8829 (pt) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1483 time to fit residues: 24.4135 Evaluate side-chains 78 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 7.9990 chunk 273 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 232 optimal weight: 0.0270 chunk 15 optimal weight: 40.0000 chunk 234 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 231 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 2.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 679 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.039684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.027425 restraints weight = 403719.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.028135 restraints weight = 302497.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.028688 restraints weight = 243028.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.029109 restraints weight = 204596.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.029438 restraints weight = 178575.079| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3894 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= 0.127 Angle : 0.649 9.677 33098 Z= 0.338 Chirality : 0.044 0.225 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.435 172.019 3888 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -2.55 (0.15), residues: 2837 helix: 0.24 (0.17), residues: 893 sheet: -2.14 (0.30), residues: 280 loop : -2.88 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 414 TYR 0.033 0.002 TYR H 101 PHE 0.025 0.001 PHE N 375 TRP 0.020 0.002 TRP N 346 HIS 0.006 0.001 HIS O 417 Details of bonding type rmsd covalent geometry : bond 0.00264 (24149) covalent geometry : angle 0.64893 (33098) hydrogen bonds : bond 0.03604 ( 806) hydrogen bonds : angle 6.06245 ( 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 103 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.614 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: 0.8350 (tt) cc_final: 0.7917 (tt) REVERT: A 1006 MET cc_start: 0.9253 (ttt) cc_final: 0.9052 (ptm) REVERT: N 551 MET cc_start: 0.5502 (pmm) cc_final: 0.5009 (pmm) REVERT: N 638 ASN cc_start: 0.8448 (m110) cc_final: 0.7999 (t0) REVERT: N 649 MET cc_start: 0.7756 (tpt) cc_final: 0.7477 (tpt) REVERT: O 551 MET cc_start: 0.6857 (tmm) cc_final: 0.6614 (tmm) REVERT: O 648 LEU cc_start: 0.8756 (tp) cc_final: 0.8494 (pt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1468 time to fit residues: 24.6370 Evaluate side-chains 80 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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: 0.5980 chunk 234 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 197 optimal weight: 40.0000 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 173 optimal weight: 30.0000 chunk 115 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 246 optimal weight: 0.5980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN F 89 HIS ** H 328 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 679 GLN ** 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 = 0.3439 r_free = 0.3439 target = 0.039905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.027528 restraints weight = 400743.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.028240 restraints weight = 301427.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.028780 restraints weight = 242598.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.029210 restraints weight = 205121.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.029537 restraints weight = 179247.652| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24149 Z= 0.119 Angle : 0.634 8.992 33098 Z= 0.328 Chirality : 0.044 0.226 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.234 170.672 3888 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -2.35 (0.16), residues: 2837 helix: 0.50 (0.18), residues: 893 sheet: -2.12 (0.30), residues: 286 loop : -2.80 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 602 TYR 0.033 0.002 TYR O 564 PHE 0.019 0.001 PHE N 375 TRP 0.019 0.002 TRP N 346 HIS 0.007 0.001 HIS O 417 Details of bonding type rmsd covalent geometry : bond 0.00249 (24149) covalent geometry : angle 0.63449 (33098) hydrogen bonds : bond 0.03417 ( 806) hydrogen bonds : angle 5.87550 ( 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 101 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.584 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: 0.8393 (tt) cc_final: 0.7982 (tt) REVERT: A 370 MET cc_start: 0.3572 (ppp) cc_final: 0.3352 (ppp) REVERT: N 411 ASN cc_start: 0.9875 (t0) cc_final: 0.9515 (m110) REVERT: N 551 MET cc_start: 0.5454 (pmm) cc_final: 0.4878 (pmm) REVERT: N 638 ASN cc_start: 0.8532 (m110) cc_final: 0.8086 (t0) REVERT: N 649 MET cc_start: 0.7705 (tpt) cc_final: 0.7481 (tpt) REVERT: O 515 MET cc_start: 0.7512 (ttm) cc_final: 0.7223 (tpp) REVERT: O 551 MET cc_start: 0.7045 (tmm) cc_final: 0.6536 (tmm) REVERT: O 648 LEU cc_start: 0.8819 (tp) cc_final: 0.8556 (pp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1440 time to fit residues: 23.9567 Evaluate side-chains 81 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 7.9990 chunk 67 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.0270 chunk 11 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 87 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 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 559 GLN N 679 GLN ** 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 = 0.3405 r_free = 0.3405 target = 0.039090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.027018 restraints weight = 408754.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.027694 restraints weight = 309461.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.028198 restraints weight = 250462.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.028588 restraints weight = 212839.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.028902 restraints weight = 187284.550| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24149 Z= 0.169 Angle : 0.681 9.106 33098 Z= 0.355 Chirality : 0.045 0.183 3762 Planarity : 0.004 0.054 4040 Dihedral : 13.334 168.707 3888 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % 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: -2.45 (0.15), residues: 2837 helix: 0.30 (0.17), residues: 894 sheet: -1.94 (0.32), residues: 261 loop : -2.84 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.030 0.002 TYR H 101 PHE 0.022 0.002 PHE N 612 TRP 0.016 0.002 TRP N 346 HIS 0.007 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00348 (24149) covalent geometry : angle 0.68143 (33098) hydrogen bonds : bond 0.03774 ( 806) hydrogen bonds : angle 6.10687 ( 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 97 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.793 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: A 265 LEU cc_start: 0.8330 (tt) cc_final: 0.7935 (tt) REVERT: N 551 MET cc_start: 0.5638 (pmm) cc_final: 0.5124 (pmm) REVERT: O 515 MET cc_start: 0.7694 (ttm) cc_final: 0.7406 (tpp) REVERT: O 551 MET cc_start: 0.7173 (tmm) cc_final: 0.6659 (tmm) REVERT: O 648 LEU cc_start: 0.8893 (tp) cc_final: 0.8624 (pp) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.1628 time to fit residues: 26.0292 Evaluate side-chains 80 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 0.0040 chunk 149 optimal weight: 0.0270 chunk 208 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 271 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 240 optimal weight: 0.0970 chunk 246 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 157 optimal weight: 40.0000 overall best weight: 1.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 F 89 HIS ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 388 HIS N 583 ASN N 638 ASN N 679 GLN O 489 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.040270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.027779 restraints weight = 396788.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.028519 restraints weight = 297356.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.029086 restraints weight = 238260.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.029516 restraints weight = 200722.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.029852 restraints weight = 175277.251| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24149 Z= 0.111 Angle : 0.626 9.196 33098 Z= 0.323 Chirality : 0.044 0.175 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.052 168.206 3888 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -2.27 (0.16), residues: 2837 helix: 0.53 (0.17), residues: 907 sheet: -2.00 (0.30), residues: 282 loop : -2.76 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 616 TYR 0.031 0.001 TYR O 564 PHE 0.019 0.001 PHE H 129 TRP 0.020 0.001 TRP N 346 HIS 0.006 0.001 HIS O 417 Details of bonding type rmsd covalent geometry : bond 0.00235 (24149) covalent geometry : angle 0.62571 (33098) hydrogen bonds : bond 0.03296 ( 806) hydrogen bonds : angle 5.77056 ( 2301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5575.60 seconds wall clock time: 96 minutes 43.68 seconds (5803.68 seconds total)