Starting phenix.real_space_refine on Sun Sep 13 03:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy7_11553/09_2026/6zy7_11553.cif" } resolution = 4.64 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= 0.004 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 62 5.49 5 S 92 5.16 5 C 12527 2.51 5 N 3417 2.21 5 O 3881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19979 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 9310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9310 Classifications: {'peptide': 1160} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 1114} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 9305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9305 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 1113} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.23 Number of scatterers: 19979 At special positions: 0 Unit cell: (119.053, 116.039, 197.417, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 62 15.00 O 3881 8.00 N 3417 7.00 C 12527 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: 4.09 Conformation dependent library (CDL) restraints added in 843.3 milliseconds 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 26 sheets defined 46.4% alpha, 10.9% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.799A pdb=" N ILE B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 99 removed outlier: 4.052A pdb=" N ILE B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.839A pdb=" N CYS B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.529A pdb=" N PHE B 226 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 227 " --> pdb=" O SER B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 227' Processing helix chain 'B' and resid 232 through 250 removed outlier: 3.519A pdb=" N ASP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.806A pdb=" N SER B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 342 removed outlier: 4.137A pdb=" N ASP B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.636A pdb=" N PHE B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.907A pdb=" N ILE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 431 removed outlier: 3.796A pdb=" N GLN B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.891A pdb=" N THR B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 504 through 515 removed outlier: 4.019A pdb=" N ASN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.587A pdb=" N LEU B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.507A pdb=" N SER B 547 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.576A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 567 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.677A pdb=" N HIS B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.758A pdb=" N ALA B 647 " --> pdb=" O PRO B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 679 removed outlier: 3.594A pdb=" N PHE B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 Processing helix chain 'B' and resid 702 through 714 Processing helix chain 'B' and resid 723 through 736 removed outlier: 3.546A pdb=" N VAL B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 Processing helix chain 'B' and resid 760 through 771 removed outlier: 3.774A pdb=" N MET B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 819 through 823 removed outlier: 4.069A pdb=" N ASP B 823 " --> pdb=" O PRO B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 868 through 882 removed outlier: 3.726A pdb=" N ASP B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 882 " --> pdb=" O ARG B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 945 removed outlier: 4.588A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix removed outlier: 3.778A pdb=" N ASN B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 984 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1014 through 1028 removed outlier: 3.649A pdb=" N ILE B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1061 removed outlier: 4.800A pdb=" N GLY B1039 " --> pdb=" O GLU B1035 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1040 " --> pdb=" O TRP B1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B1042 " --> pdb=" O LEU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1080 removed outlier: 3.640A pdb=" N GLN B1079 " --> pdb=" O LYS B1075 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B1080 " --> pdb=" O VAL B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1096 Processing helix chain 'B' and resid 1132 through 1136 Processing helix chain 'B' and resid 1137 through 1161 removed outlier: 3.998A pdb=" N GLU B1143 " --> pdb=" O GLU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1193 removed outlier: 4.090A pdb=" N LEU B1166 " --> pdb=" O SER B1162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP B1167 " --> pdb=" O PRO B1163 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B1168 " --> pdb=" O SER B1164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B1180 " --> pdb=" O GLU B1176 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B1189 " --> pdb=" O GLU B1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.790A pdb=" N ILE A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 removed outlier: 3.539A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.723A pdb=" N CYS A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 250 removed outlier: 3.624A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.802A pdb=" N ASP A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 343 removed outlier: 3.512A pdb=" N VAL A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.972A pdb=" N VAL A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.546A pdb=" N PHE A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.976A pdb=" N ILE A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 430 removed outlier: 3.555A pdb=" N LYS A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.891A pdb=" N THR A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.019A pdb=" N ASN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.588A pdb=" N LEU A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.507A pdb=" N SER A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.576A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.678A pdb=" N HIS A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.759A pdb=" N ALA A 647 " --> pdb=" O PRO A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 679 removed outlier: 3.596A pdb=" N PHE A 668 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 702 Processing helix chain 'A' and resid 702 through 714 Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.546A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 760 through 771 removed outlier: 3.772A pdb=" N MET A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 819 through 823 removed outlier: 4.071A pdb=" N ASP A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.726A pdb=" N ASP A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 removed outlier: 4.588A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix removed outlier: 3.778A pdb=" N ASN A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 1014 through 1028 removed outlier: 3.648A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1061 removed outlier: 4.798A pdb=" N GLY A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1080 removed outlier: 3.605A pdb=" N GLN A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1096 Processing helix chain 'A' and resid 1132 through 1136 Processing helix chain 'A' and resid 1137 through 1161 removed outlier: 3.998A pdb=" N GLU A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1193 removed outlier: 4.074A pdb=" N LYS A1168 " --> pdb=" O SER A1164 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1180 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.639A pdb=" N SER A 148 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 65 removed outlier: 3.602A pdb=" N ARG B 73 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 65 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 207 removed outlier: 3.750A pdb=" N GLN B 192 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 176 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 219 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 116 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AA6, first strand: chain 'B' and resid 290 through 294 removed outlier: 5.826A pdb=" N GLN B 292 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL B 299 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 300 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 309 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 364 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 311 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 322 through 323 removed outlier: 7.248A pdb=" N GLY B 322 " --> pdb=" O MET B 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 483 through 485 removed outlier: 6.594A pdb=" N ILE B 458 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU B 459 " --> pdb=" O MET B 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 588 through 589 removed outlier: 3.551A pdb=" N VAL B 578 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AB2, first strand: chain 'B' and resid 853 through 856 Processing sheet with id=AB3, first strand: chain 'B' and resid 898 through 901 Processing sheet with id=AB4, first strand: chain 'B' and resid 956 through 959 removed outlier: 6.340A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS B1203 " --> pdb=" O ILE B 915 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.622A pdb=" N LEU B1002 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 57 through 65 removed outlier: 3.635A pdb=" N PHE A 77 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 61 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 73 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 65 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 188 through 193 removed outlier: 3.646A pdb=" N PHE A 190 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 181 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 192 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 116 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 105 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AB9, first strand: chain 'A' and resid 290 through 294 removed outlier: 5.884A pdb=" N GLN A 292 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 299 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 298 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 300 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN A 309 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N VAL A 364 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 290 through 294 removed outlier: 5.884A pdb=" N GLN A 292 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 299 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 298 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 300 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 483 through 485 removed outlier: 6.594A pdb=" N ILE A 458 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 459 " --> pdb=" O MET A 539 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 588 through 589 removed outlier: 3.551A pdb=" N VAL A 578 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AC5, first strand: chain 'A' and resid 853 through 856 Processing sheet with id=AC6, first strand: chain 'A' and resid 898 through 901 Processing sheet with id=AC7, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.342A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A1203 " --> pdb=" O ILE A 915 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1001 through 1002 removed outlier: 3.620A pdb=" N LEU A1002 " --> pdb=" O LYS A1010 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3464 1.32 - 1.45: 5374 1.45 - 1.57: 11393 1.57 - 1.69: 122 1.69 - 1.82: 158 Bond restraints: 20511 Sorted by residual: bond pdb=" N3B ANP B1601 " pdb=" PG ANP B1601 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N3B ANP A1601 " pdb=" PG ANP A1601 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" O3A ANP B1601 " pdb=" PB ANP B1601 " ideal model delta sigma weight residual 1.700 1.599 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3A ANP A1601 " pdb=" PB ANP A1601 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ILE B 864 " pdb=" CA ILE B 864 " ideal model delta sigma weight residual 1.454 1.485 -0.031 7.70e-03 1.69e+04 1.57e+01 ... (remaining 20506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 26591 2.17 - 4.33: 1304 4.33 - 6.50: 40 6.50 - 8.66: 5 8.66 - 10.83: 3 Bond angle restraints: 27943 Sorted by residual: angle pdb=" CA HIS B 605 " pdb=" C HIS B 605 " pdb=" O HIS B 605 " ideal model delta sigma weight residual 121.47 116.88 4.59 1.15e+00 7.56e-01 1.59e+01 angle pdb=" CA HIS A 605 " pdb=" C HIS A 605 " pdb=" O HIS A 605 " ideal model delta sigma weight residual 121.47 116.89 4.58 1.15e+00 7.56e-01 1.59e+01 angle pdb=" N VAL B1191 " pdb=" CA VAL B1191 " pdb=" C VAL B1191 " ideal model delta sigma weight residual 110.72 106.72 4.00 1.01e+00 9.80e-01 1.57e+01 angle pdb=" N VAL A1191 " pdb=" CA VAL A1191 " pdb=" C VAL A1191 " ideal model delta sigma weight residual 110.72 106.78 3.94 1.01e+00 9.80e-01 1.52e+01 angle pdb=" C LYS B 606 " pdb=" CA LYS B 606 " pdb=" CB LYS B 606 " ideal model delta sigma weight residual 109.83 113.67 -3.84 9.90e-01 1.02e+00 1.51e+01 ... (remaining 27938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 11829 28.12 - 56.23: 336 56.23 - 84.35: 53 84.35 - 112.47: 3 112.47 - 140.58: 2 Dihedral angle restraints: 12223 sinusoidal: 5472 harmonic: 6751 Sorted by residual: dihedral pdb=" C4' DC C 9 " pdb=" C3' DC C 9 " pdb=" O3' DC C 9 " pdb=" P DG C 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.42 140.58 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " pdb=" O3' DC E 9 " pdb=" P DG E 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.45 140.55 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C TYR B 830 " pdb=" N TYR B 830 " pdb=" CA TYR B 830 " pdb=" CB TYR B 830 " ideal model delta harmonic sigma weight residual -122.60 -131.78 9.18 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 12220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1871 0.057 - 0.114: 774 0.114 - 0.171: 325 0.171 - 0.228: 95 0.228 - 0.285: 16 Chirality restraints: 3081 Sorted by residual: chirality pdb=" CA ILE B 915 " pdb=" N ILE B 915 " pdb=" C ILE B 915 " pdb=" CB ILE B 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' ANP B1601 " pdb=" C2' ANP B1601 " pdb=" C4' ANP B1601 " pdb=" O3' ANP B1601 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3078 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 824 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C HIS B 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS B 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 824 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C HIS A 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS A 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 815 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ARG B 815 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 815 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 816 " 0.014 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2188 2.75 - 3.29: 19518 3.29 - 3.83: 31301 3.83 - 4.36: 38361 4.36 - 4.90: 62504 Nonbonded interactions: 153872 Sorted by model distance: nonbonded pdb=" O6 DG E 13 " pdb=" O13 EVP F 101 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 312 " pdb=" OG1 THR A 319 " model vdw 2.300 3.040 nonbonded pdb=" ND2 ASN B 315 " pdb=" O ILE B 368 " model vdw 2.331 3.120 nonbonded pdb=" OG SER A 304 " pdb=" O GLY A 307 " model vdw 2.337 3.040 nonbonded pdb=" OH TYR A 270 " pdb=" OH TYR A 274 " model vdw 2.341 3.040 ... (remaining 153867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 29 through 345 or resid 351 through 1601)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 21.630 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.009 0.165 20511 Z= 0.665 Angle : 1.007 10.829 27943 Z= 0.742 Chirality : 0.076 0.285 3081 Planarity : 0.006 0.038 3339 Dihedral : 12.482 140.584 7869 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2307 helix: 0.43 (0.17), residues: 912 sheet: -1.68 (0.29), residues: 343 loop : -2.40 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 804 TYR 0.022 0.002 TYR A 830 PHE 0.010 0.001 PHE B 417 TRP 0.023 0.002 TRP B1167 HIS 0.004 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.67 (20511) covalent geometry : angle 1.00746 / 0.74 (27943) hydrogen bonds : bond 0.21858 / 14.28 ( 804) hydrogen bonds : angle 6.85707 / 4.70 ( 2210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.4539 (ptm) cc_final: 0.4239 (ppp) REVERT: B 228 MET cc_start: 0.8887 (mtp) cc_final: 0.8655 (mtm) REVERT: B 718 MET cc_start: 0.9193 (ptm) cc_final: 0.8826 (ptt) REVERT: B 805 TYR cc_start: 0.8514 (m-10) cc_final: 0.7797 (m-10) REVERT: B 809 MET cc_start: 0.9488 (ttp) cc_final: 0.9050 (mmm) REVERT: A 61 MET cc_start: 0.5117 (ptm) cc_final: 0.4887 (pmm) REVERT: A 459 LEU cc_start: 0.9446 (mt) cc_final: 0.9200 (mm) REVERT: A 539 MET cc_start: 0.9284 (ptm) cc_final: 0.8974 (ppp) REVERT: A 809 MET cc_start: 0.9243 (ttp) cc_final: 0.8851 (ttm) REVERT: A 831 ASP cc_start: 0.9513 (m-30) cc_final: 0.9219 (p0) REVERT: A 949 LYS cc_start: 0.9606 (pttt) cc_final: 0.9385 (ptpp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1998 time to fit residues: 45.8969 Evaluate side-chains 103 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 558 HIS B 634 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 HIS A 634 HIS ** A 746 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 = 0.3321 r_free = 0.3321 target = 0.042137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.026297 restraints weight = 294699.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027158 restraints weight = 167363.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.027661 restraints weight = 114816.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028046 restraints weight = 88562.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.028308 restraints weight = 74032.705| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 20511 Z= 0.143 Angle : 0.558 13.344 27943 Z= 0.302 Chirality : 0.041 0.224 3081 Planarity : 0.004 0.055 3339 Dihedral : 15.932 137.949 3141 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2307 helix: 0.92 (0.18), residues: 916 sheet: -1.64 (0.28), residues: 358 loop : -2.08 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 835 TYR 0.016 0.001 TYR A 830 PHE 0.014 0.001 PHE B 417 TRP 0.021 0.002 TRP B1090 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (20511) covalent geometry : angle 0.55829 / 0.30 (27943) hydrogen bonds : bond 0.05034 / 3.22 ( 804) hydrogen bonds : angle 4.86487 / 3.36 ( 2210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.782 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: B 718 MET cc_start: 0.9085 (ptm) cc_final: 0.8812 (ptt) REVERT: B 943 MET cc_start: 0.8625 (tpt) cc_final: 0.8388 (tpt) REVERT: A 61 MET cc_start: 0.6168 (ptm) cc_final: 0.5957 (pmm) REVERT: A 718 MET cc_start: 0.8576 (ptp) cc_final: 0.8218 (ptt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1850 time to fit residues: 29.4330 Evaluate side-chains 86 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 154 optimal weight: 40.0000 chunk 135 optimal weight: 40.0000 chunk 117 optimal weight: 30.0000 chunk 176 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 824 HIS A 171 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 667 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 824 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.040470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.026556 restraints weight = 307361.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.027162 restraints weight = 196347.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.027466 restraints weight = 141389.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.027626 restraints weight = 114413.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.027856 restraints weight = 100683.940| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20511 Z= 0.188 Angle : 0.579 9.049 27943 Z= 0.309 Chirality : 0.040 0.226 3081 Planarity : 0.004 0.054 3339 Dihedral : 16.039 143.029 3141 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2307 helix: 1.11 (0.17), residues: 935 sheet: -1.72 (0.28), residues: 366 loop : -1.89 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.018 0.001 TYR A 830 PHE 0.017 0.002 PHE B 417 TRP 0.017 0.002 TRP B1036 HIS 0.006 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (20511) covalent geometry : angle 0.57882 / 0.31 (27943) hydrogen bonds : bond 0.04601 / 2.97 ( 804) hydrogen bonds : angle 4.65388 / 3.20 ( 2210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.769 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: B 135 MET cc_start: 0.5573 (ptm) cc_final: 0.5170 (ppp) REVERT: B 204 MET cc_start: 0.5615 (ttt) cc_final: 0.4935 (tpt) REVERT: B 718 MET cc_start: 0.8960 (ptm) cc_final: 0.8720 (ptt) REVERT: B 766 MET cc_start: 0.9480 (ptp) cc_final: 0.9228 (ptp) REVERT: A 61 MET cc_start: 0.5564 (ptm) cc_final: 0.5290 (pmm) REVERT: A 102 MET cc_start: 0.6672 (tpt) cc_final: 0.6298 (tpt) REVERT: A 198 MET cc_start: 0.7912 (mtt) cc_final: 0.7456 (mmm) REVERT: A 537 MET cc_start: 0.7327 (tpp) cc_final: 0.7112 (tpp) REVERT: A 539 MET cc_start: 0.9058 (ppp) cc_final: 0.8853 (ppp) REVERT: A 972 MET cc_start: 0.9007 (pmm) cc_final: 0.8307 (pmm) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1690 time to fit residues: 23.7013 Evaluate side-chains 82 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 170 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 151 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.040745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.025024 restraints weight = 305802.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.025833 restraints weight = 175520.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.026402 restraints weight = 120915.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.026759 restraints weight = 92217.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.026962 restraints weight = 76923.329| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20511 Z= 0.105 Angle : 0.480 12.345 27943 Z= 0.258 Chirality : 0.039 0.170 3081 Planarity : 0.003 0.053 3339 Dihedral : 16.024 141.885 3141 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2307 helix: 1.31 (0.18), residues: 938 sheet: -1.66 (0.28), residues: 371 loop : -1.79 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.013 0.001 TYR A 830 PHE 0.014 0.001 PHE B 417 TRP 0.011 0.001 TRP A 414 HIS 0.002 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (20511) covalent geometry : angle 0.48014 / 0.26 (27943) hydrogen bonds : bond 0.03392 / 2.18 ( 804) hydrogen bonds : angle 4.40227 / 3.02 ( 2210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.684 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: B 135 MET cc_start: 0.7152 (ptm) cc_final: 0.6927 (ppp) REVERT: B 204 MET cc_start: 0.7113 (ttt) cc_final: 0.6776 (tpt) REVERT: B 718 MET cc_start: 0.9107 (ptm) cc_final: 0.8864 (ptt) REVERT: B 766 MET cc_start: 0.8976 (ptp) cc_final: 0.8762 (ptp) REVERT: A 61 MET cc_start: 0.6436 (ptm) cc_final: 0.6217 (pmm) REVERT: A 669 MET cc_start: 0.9665 (ppp) cc_final: 0.9444 (ppp) REVERT: A 718 MET cc_start: 0.8710 (ptp) cc_final: 0.8343 (ptt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1527 time to fit residues: 22.2104 Evaluate side-chains 80 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 42 optimal weight: 30.0000 chunk 116 optimal weight: 30.0000 chunk 232 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 220 optimal weight: 0.0970 chunk 64 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 226 optimal weight: 30.0000 chunk 230 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.039680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024339 restraints weight = 310883.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.025094 restraints weight = 179087.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025533 restraints weight = 124524.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.025905 restraints weight = 96764.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026141 restraints weight = 81256.554| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20511 Z= 0.136 Angle : 0.493 7.241 27943 Z= 0.267 Chirality : 0.039 0.167 3081 Planarity : 0.003 0.052 3339 Dihedral : 16.065 142.058 3141 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2307 helix: 1.38 (0.18), residues: 952 sheet: -1.63 (0.28), residues: 376 loop : -1.71 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.014 0.001 TYR A 830 PHE 0.011 0.001 PHE B 417 TRP 0.012 0.001 TRP B1036 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (20511) covalent geometry : angle 0.49309 / 0.27 (27943) hydrogen bonds : bond 0.03515 / 2.28 ( 804) hydrogen bonds : angle 4.31313 / 2.95 ( 2210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.772 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: B 135 MET cc_start: 0.6825 (ptm) cc_final: 0.6594 (ppp) REVERT: B 204 MET cc_start: 0.7184 (ttt) cc_final: 0.6810 (tpt) REVERT: B 381 MET cc_start: 0.5009 (tpp) cc_final: 0.4754 (tpt) REVERT: B 718 MET cc_start: 0.9209 (ptm) cc_final: 0.8989 (ptt) REVERT: A 61 MET cc_start: 0.6456 (ptm) cc_final: 0.6239 (pmm) REVERT: A 189 MET cc_start: 0.4344 (tpt) cc_final: 0.4041 (tpt) REVERT: A 718 MET cc_start: 0.8753 (ptp) cc_final: 0.8315 (ptt) REVERT: A 769 ILE cc_start: 0.9691 (mt) cc_final: 0.9415 (tp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1675 time to fit residues: 23.9906 Evaluate side-chains 79 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 133 optimal weight: 40.0000 chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN A 445 ASN A 498 HIS A 508 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.039193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.023201 restraints weight = 325128.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.023828 restraints weight = 218229.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024240 restraints weight = 163861.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.024569 restraints weight = 132893.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.024805 restraints weight = 113482.734| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20511 Z= 0.147 Angle : 0.503 6.982 27943 Z= 0.275 Chirality : 0.039 0.165 3081 Planarity : 0.003 0.080 3339 Dihedral : 16.141 141.964 3141 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2307 helix: 1.50 (0.18), residues: 946 sheet: -1.41 (0.30), residues: 323 loop : -1.63 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 740 TYR 0.015 0.001 TYR A 830 PHE 0.010 0.001 PHE A 706 TRP 0.013 0.001 TRP B 931 HIS 0.009 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (20511) covalent geometry : angle 0.50305 / 0.28 (27943) hydrogen bonds : bond 0.03469 / 2.32 ( 804) hydrogen bonds : angle 4.31667 / 2.96 ( 2210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.829 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: B 135 MET cc_start: 0.6875 (ptm) cc_final: 0.6641 (ppp) REVERT: B 204 MET cc_start: 0.7219 (ttt) cc_final: 0.6768 (tpt) REVERT: B 768 ILE cc_start: 0.9479 (mt) cc_final: 0.9178 (mm) REVERT: B 1131 MET cc_start: 0.9449 (mpp) cc_final: 0.9209 (mpp) REVERT: A 61 MET cc_start: 0.6477 (ptm) cc_final: 0.6262 (pmm) REVERT: A 135 MET cc_start: 0.2604 (tpt) cc_final: 0.2302 (tmm) REVERT: A 189 MET cc_start: 0.4607 (tpt) cc_final: 0.4348 (tpt) REVERT: A 204 MET cc_start: 0.6896 (mmm) cc_final: 0.6544 (tpt) REVERT: A 718 MET cc_start: 0.8728 (ptp) cc_final: 0.8458 (ptt) REVERT: A 769 ILE cc_start: 0.9703 (mt) cc_final: 0.9446 (tp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1680 time to fit residues: 23.7870 Evaluate side-chains 80 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 186 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 ASN B 150 ASN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 HIS B 746 GLN B 938 GLN B1051 GLN A 91 ASN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 567 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.036108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.021208 restraints weight = 335685.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.021755 restraints weight = 229566.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.022056 restraints weight = 174078.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.022315 restraints weight = 143847.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.022559 restraints weight = 124229.311| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 20511 Z= 0.323 Angle : 0.823 18.369 27943 Z= 0.431 Chirality : 0.045 0.325 3081 Planarity : 0.006 0.170 3339 Dihedral : 16.553 144.945 3141 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2307 helix: 0.49 (0.16), residues: 952 sheet: -1.64 (0.30), residues: 321 loop : -1.76 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG B1020 TYR 0.040 0.003 TYR A 830 PHE 0.055 0.003 PHE B1023 TRP 0.029 0.003 TRP B 931 HIS 0.011 0.002 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.32 (20511) covalent geometry : angle 0.82330 / 0.43 (27943) hydrogen bonds : bond 0.06694 / 4.48 ( 804) hydrogen bonds : angle 4.97224 / 3.41 ( 2210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.939 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: B 135 MET cc_start: 0.7106 (ptm) cc_final: 0.6847 (ppp) REVERT: B 204 MET cc_start: 0.7724 (ttt) cc_final: 0.7361 (tpt) REVERT: B 847 MET cc_start: 0.9503 (mmp) cc_final: 0.9299 (mmm) REVERT: B 1131 MET cc_start: 0.9374 (mpp) cc_final: 0.9124 (mpp) REVERT: A 204 MET cc_start: 0.7127 (mmm) cc_final: 0.6794 (tpt) REVERT: A 718 MET cc_start: 0.8671 (ptp) cc_final: 0.8419 (ptt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1642 time to fit residues: 21.9181 Evaluate side-chains 75 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 220 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 218 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.037512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.022136 restraints weight = 327317.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.022724 restraints weight = 214543.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.023088 restraints weight = 160108.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.023374 restraints weight = 130203.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.023595 restraints weight = 111275.541| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20511 Z= 0.135 Angle : 0.558 7.987 27943 Z= 0.299 Chirality : 0.041 0.225 3081 Planarity : 0.004 0.053 3339 Dihedral : 16.509 144.922 3141 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2307 helix: 1.03 (0.17), residues: 960 sheet: -1.58 (0.30), residues: 318 loop : -1.64 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 635 TYR 0.021 0.001 TYR A 830 PHE 0.018 0.002 PHE A 731 TRP 0.027 0.002 TRP B 931 HIS 0.003 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (20511) covalent geometry : angle 0.55800 / 0.30 (27943) hydrogen bonds : bond 0.03473 / 2.30 ( 804) hydrogen bonds : angle 4.62338 / 3.16 ( 2210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.7089 (ptm) cc_final: 0.6872 (ppp) REVERT: B 204 MET cc_start: 0.7729 (ttt) cc_final: 0.7381 (tpt) REVERT: A 189 MET cc_start: 0.4712 (tpt) cc_final: 0.4399 (tpt) REVERT: A 537 MET cc_start: 0.7157 (tpp) cc_final: 0.6948 (tpp) REVERT: A 669 MET cc_start: 0.9659 (ppp) cc_final: 0.9368 (ppp) REVERT: A 718 MET cc_start: 0.8760 (ptp) cc_final: 0.8476 (ptt) REVERT: A 769 ILE cc_start: 0.9681 (mt) cc_final: 0.9416 (tp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1492 time to fit residues: 20.3774 Evaluate side-chains 77 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 179 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 226 optimal weight: 30.0000 chunk 181 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 961 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 = 0.3192 r_free = 0.3192 target = 0.037437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.022073 restraints weight = 328039.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.022685 restraints weight = 215499.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023011 restraints weight = 159865.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.023374 restraints weight = 129421.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.023520 restraints weight = 110988.562| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20511 Z= 0.129 Angle : 0.541 12.363 27943 Z= 0.287 Chirality : 0.040 0.209 3081 Planarity : 0.004 0.053 3339 Dihedral : 16.441 144.190 3141 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2307 helix: 1.27 (0.17), residues: 954 sheet: -1.55 (0.30), residues: 330 loop : -1.50 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 672 TYR 0.016 0.001 TYR A 830 PHE 0.022 0.002 PHE A 668 TRP 0.021 0.002 TRP B 931 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (20511) covalent geometry : angle 0.54081 / 0.29 (27943) hydrogen bonds : bond 0.03481 / 2.31 ( 804) hydrogen bonds : angle 4.49170 / 3.08 ( 2210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.781 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: B 135 MET cc_start: 0.7105 (ptm) cc_final: 0.6890 (ppp) REVERT: B 204 MET cc_start: 0.7721 (ttt) cc_final: 0.7371 (tpt) REVERT: B 381 MET cc_start: 0.4951 (tpp) cc_final: 0.4748 (tpt) REVERT: A 189 MET cc_start: 0.4798 (tpt) cc_final: 0.4468 (tpt) REVERT: A 718 MET cc_start: 0.8783 (ptp) cc_final: 0.8482 (ptt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1413 time to fit residues: 19.3432 Evaluate side-chains 76 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 224 optimal weight: 0.0060 chunk 42 optimal weight: 30.0000 chunk 182 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.037652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.021970 restraints weight = 329721.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.022539 restraints weight = 220967.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.022956 restraints weight = 168023.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.023220 restraints weight = 135685.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.023460 restraints weight = 117068.422| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20511 Z= 0.110 Angle : 0.503 8.351 27943 Z= 0.270 Chirality : 0.039 0.209 3081 Planarity : 0.003 0.045 3339 Dihedral : 16.400 143.991 3141 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2307 helix: 1.25 (0.17), residues: 970 sheet: -1.53 (0.30), residues: 330 loop : -1.51 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 740 TYR 0.013 0.001 TYR A 830 PHE 0.013 0.001 PHE A 731 TRP 0.022 0.002 TRP B 931 HIS 0.003 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (20511) covalent geometry : angle 0.50341 / 0.27 (27943) hydrogen bonds : bond 0.03033 / 2.01 ( 804) hydrogen bonds : angle 4.39910 / 3.02 ( 2210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.7112 (ptm) cc_final: 0.6899 (ppp) REVERT: B 204 MET cc_start: 0.7696 (ttt) cc_final: 0.7331 (tpt) REVERT: B 718 MET cc_start: 0.9449 (ptp) cc_final: 0.9170 (ptp) REVERT: B 766 MET cc_start: 0.9611 (mpp) cc_final: 0.9376 (mpp) REVERT: B 1131 MET cc_start: 0.8877 (mpp) cc_final: 0.8655 (mpp) REVERT: A 189 MET cc_start: 0.4791 (tpt) cc_final: 0.4557 (tpt) REVERT: A 718 MET cc_start: 0.8779 (ptp) cc_final: 0.8483 (ptt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1457 time to fit residues: 19.6815 Evaluate side-chains 76 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 160 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 203 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 91 optimal weight: 0.4980 chunk 85 optimal weight: 0.0170 chunk 153 optimal weight: 20.0000 overall best weight: 4.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.036593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.021491 restraints weight = 335064.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.022055 restraints weight = 221129.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.022419 restraints weight = 164086.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.022694 restraints weight = 133531.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.022893 restraints weight = 114371.414| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20511 Z= 0.175 Angle : 0.582 10.740 27943 Z= 0.310 Chirality : 0.040 0.227 3081 Planarity : 0.004 0.060 3339 Dihedral : 16.470 144.561 3141 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2307 helix: 1.17 (0.17), residues: 964 sheet: -1.48 (0.31), residues: 318 loop : -1.50 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 672 TYR 0.022 0.002 TYR A 830 PHE 0.018 0.002 PHE B 807 TRP 0.026 0.002 TRP B 931 HIS 0.009 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (20511) covalent geometry : angle 0.58158 / 0.31 (27943) hydrogen bonds : bond 0.04070 / 2.72 ( 804) hydrogen bonds : angle 4.55290 / 3.14 ( 2210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4642.71 seconds wall clock time: 80 minutes 47.57 seconds (4847.57 seconds total)