Starting phenix.real_space_refine on Sat Jul 4 11:36:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy7_11553/07_2026/6zy7_11553.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy7_11553/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy7_11553/07_2026/6zy7_11553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy7_11553/07_2026/6zy7_11553.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy7_11553/07_2026/6zy7_11553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy7_11553/07_2026/6zy7_11553.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zy7_11553/07_2026/6zy7_11553.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy7_11553/07_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-dev-6108/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: 3.89, per 1000 atoms: 0.19 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: 1.58 Conformation dependent library (CDL) restraints added in 705.0 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: 2.01 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: 4.09 Time building geometry restraints manager: 2.17 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: 26593 2.17 - 4.33: 1302 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 18.800 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- 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 / 0.66 (20511) covalent geometry : angle 1.00708 / 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 : 0.595 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: 0.1686 time to fit residues: 38.6017 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 : 0.609 ------------------------------------------------------------------------------- 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 = 0.042153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.026313 restraints weight = 294503.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.027160 restraints weight = 167946.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.027674 restraints weight = 115313.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028068 restraints weight = 89396.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028239 restraints weight = 74403.100| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20511 Z= 0.142 Angle : 0.548 13.253 27943 Z= 0.297 Chirality : 0.041 0.214 3081 Planarity : 0.004 0.056 3339 Dihedral : 15.944 138.785 3141 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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 : -2.09 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.016 0.001 TYR A 830 PHE 0.015 0.001 PHE B 417 TRP 0.018 0.002 TRP B1090 HIS 0.003 0.001 HIS B 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (20511) covalent geometry : angle 0.54774 / 0.30 (27943) hydrogen bonds : bond 0.04972 / 3.17 ( 804) hydrogen bonds : angle 4.86451 / 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 : 0.727 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: 0.9079 (ptm) cc_final: 0.8804 (ptt) REVERT: B 943 MET cc_start: 0.8611 (tpt) cc_final: 0.8374 (tpt) REVERT: A 61 MET cc_start: 0.6168 (ptm) cc_final: 0.5958 (pmm) REVERT: A 718 MET cc_start: 0.8487 (ptp) cc_final: 0.8094 (ptt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1929 time to fit residues: 30.7525 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 : 0.696 ------------------------------------------------------------------------------- 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: 50.0000 chunk 135 optimal weight: 40.0000 chunk 117 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 196 optimal weight: 0.0980 chunk 20 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 HIS B 508 ASN ** 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 498 HIS A 508 ASN A 667 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.039463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.024226 restraints weight = 313336.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.024992 restraints weight = 181617.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.025432 restraints weight = 126153.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.025765 restraints weight = 98683.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026024 restraints weight = 83373.362| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20511 Z= 0.213 Angle : 0.621 8.436 27943 Z= 0.330 Chirality : 0.041 0.255 3081 Planarity : 0.004 0.056 3339 Dihedral : 16.099 143.999 3141 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.05 % Allowed : 1.32 % Favored : 98.63 % 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: -1.00 (0.18), residues: 2307 helix: 1.04 (0.17), residues: 939 sheet: -1.78 (0.28), residues: 376 loop : -1.89 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.019 0.002 TYR A 830 PHE 0.016 0.002 PHE B 417 TRP 0.019 0.002 TRP B1036 HIS 0.006 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (20511) covalent geometry : angle 0.62127 / 0.33 (27943) hydrogen bonds : bond 0.04881 / 3.17 ( 804) hydrogen bonds : angle 4.70311 / 3.23 ( 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 89 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.814 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: 0.6771 (ptm) cc_final: 0.6513 (ppp) REVERT: B 204 MET cc_start: 0.6673 (ttt) cc_final: 0.6283 (tpt) REVERT: B 718 MET cc_start: 0.9163 (ptm) cc_final: 0.8910 (ptt) REVERT: A 61 MET cc_start: 0.6427 (ptm) cc_final: 0.6202 (pmm) REVERT: A 198 MET cc_start: 0.8596 (mtt) cc_final: 0.8396 (mmt) REVERT: A 718 MET cc_start: 0.8833 (ptp) cc_final: 0.8563 (ptt) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1578 time to fit residues: 22.0765 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 : 0.666 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** A 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.039908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.023791 restraints weight = 320639.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024436 restraints weight = 214722.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.024841 restraints weight = 160202.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.025161 restraints weight = 130750.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025318 restraints weight = 111538.182| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20511 Z= 0.122 Angle : 0.496 9.885 27943 Z= 0.268 Chirality : 0.039 0.186 3081 Planarity : 0.003 0.054 3339 Dihedral : 16.117 142.696 3141 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.77 (0.18), residues: 2307 helix: 1.28 (0.18), residues: 945 sheet: -1.72 (0.28), residues: 371 loop : -1.81 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1033 TYR 0.017 0.001 TYR A 830 PHE 0.013 0.001 PHE B 417 TRP 0.013 0.001 TRP B 931 HIS 0.005 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (20511) covalent geometry : angle 0.49594 / 0.27 (27943) hydrogen bonds : bond 0.03507 / 2.26 ( 804) hydrogen bonds : angle 4.47698 / 3.07 ( 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 89 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.791 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: 0.6583 (ppp) REVERT: B 204 MET cc_start: 0.7119 (ttt) cc_final: 0.6790 (tpt) REVERT: B 718 MET cc_start: 0.9132 (ptm) cc_final: 0.8900 (ptt) REVERT: B 766 MET cc_start: 0.9033 (ptp) cc_final: 0.8682 (ptp) REVERT: A 61 MET cc_start: 0.6464 (ptm) cc_final: 0.6244 (pmm) REVERT: A 189 MET cc_start: 0.4291 (tpt) cc_final: 0.3993 (tpt) REVERT: A 718 MET cc_start: 0.8803 (ptp) cc_final: 0.8465 (ptt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1525 time to fit residues: 21.4737 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 : 0.649 ------------------------------------------------------------------------------- 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: 0.8980 chunk 146 optimal weight: 0.0270 chunk 220 optimal weight: 0.1980 chunk 64 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 230 optimal weight: 30.0000 chunk 152 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** 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 = 0.3254 r_free = 0.3254 target = 0.039362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.024029 restraints weight = 313397.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.024796 restraints weight = 178202.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.025225 restraints weight = 123022.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.025571 restraints weight = 96810.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.025867 restraints weight = 80598.019| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20511 Z= 0.127 Angle : 0.487 7.216 27943 Z= 0.265 Chirality : 0.039 0.163 3081 Planarity : 0.003 0.052 3339 Dihedral : 16.141 142.446 3141 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.59 (0.18), residues: 2307 helix: 1.41 (0.17), residues: 949 sheet: -1.60 (0.29), residues: 351 loop : -1.73 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.015 0.001 TYR A 830 PHE 0.011 0.001 PHE B 417 TRP 0.013 0.001 TRP B 931 HIS 0.003 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (20511) covalent geometry : angle 0.48745 / 0.26 (27943) hydrogen bonds : bond 0.03348 / 2.18 ( 804) hydrogen bonds : angle 4.34589 / 2.98 ( 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 91 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.552 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: 0.6793 (ptm) cc_final: 0.6540 (ppp) REVERT: B 204 MET cc_start: 0.7143 (ttt) cc_final: 0.6696 (tpt) REVERT: B 768 ILE cc_start: 0.9486 (mt) cc_final: 0.9280 (mt) REVERT: A 61 MET cc_start: 0.6440 (ptm) cc_final: 0.6219 (pmm) REVERT: A 135 MET cc_start: 0.2018 (tpt) cc_final: 0.1775 (tmm) REVERT: A 189 MET cc_start: 0.4926 (tpt) cc_final: 0.4674 (tpt) REVERT: A 204 MET cc_start: 0.6880 (mmm) cc_final: 0.6558 (tpt) REVERT: A 718 MET cc_start: 0.8878 (ptp) cc_final: 0.8529 (ptt) REVERT: A 769 ILE cc_start: 0.9698 (mt) cc_final: 0.9421 (tp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1519 time to fit residues: 21.3879 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 : 0.585 ------------------------------------------------------------------------------- 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: 50.0000 chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN A 171 ASN A 393 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.039501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.023286 restraints weight = 320979.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.023960 restraints weight = 212400.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.024353 restraints weight = 156985.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.024679 restraints weight = 127261.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.024947 restraints weight = 108533.495| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 20511 Z= 0.109 Angle : 0.481 11.952 27943 Z= 0.261 Chirality : 0.038 0.158 3081 Planarity : 0.003 0.052 3339 Dihedral : 16.147 142.023 3141 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -0.47 (0.18), residues: 2307 helix: 1.44 (0.18), residues: 949 sheet: -1.42 (0.30), residues: 325 loop : -1.65 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.013 0.001 TYR A 830 PHE 0.011 0.001 PHE A 573 TRP 0.011 0.001 TRP A 414 HIS 0.009 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (20511) covalent geometry : angle 0.48101 / 0.26 (27943) hydrogen bonds : bond 0.03137 / 2.09 ( 804) hydrogen bonds : angle 4.28325 / 2.92 ( 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 89 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.777 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: 0.6869 (ptm) cc_final: 0.6622 (ppp) REVERT: B 204 MET cc_start: 0.7200 (ttt) cc_final: 0.6756 (tpt) REVERT: B 768 ILE cc_start: 0.9465 (mt) cc_final: 0.9107 (mm) REVERT: B 1131 MET cc_start: 0.9420 (mpp) cc_final: 0.9173 (pmm) REVERT: A 61 MET cc_start: 0.6469 (ptm) cc_final: 0.6258 (pmm) REVERT: A 135 MET cc_start: 0.1958 (tpt) cc_final: 0.1683 (tmm) REVERT: A 204 MET cc_start: 0.6956 (mmm) cc_final: 0.6593 (tpt) REVERT: A 718 MET cc_start: 0.8838 (ptp) cc_final: 0.8515 (ptt) REVERT: A 769 ILE cc_start: 0.9685 (mt) cc_final: 0.9415 (tp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1598 time to fit residues: 22.1258 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 : 0.720 ------------------------------------------------------------------------------- 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: 10.0000 chunk 202 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 212 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 ASN B 567 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 197 ASN A 445 ASN A 567 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.037429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.022065 restraints weight = 335726.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.022608 restraints weight = 230797.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.023021 restraints weight = 175748.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.023254 restraints weight = 143615.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.023384 restraints weight = 124542.979| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 20511 Z= 0.226 Angle : 0.644 11.911 27943 Z= 0.341 Chirality : 0.041 0.247 3081 Planarity : 0.005 0.094 3339 Dihedral : 16.320 143.657 3141 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.63 (0.18), residues: 2307 helix: 1.17 (0.17), residues: 952 sheet: -1.43 (0.31), residues: 323 loop : -1.62 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1020 TYR 0.024 0.002 TYR A 830 PHE 0.034 0.002 PHE B1023 TRP 0.024 0.002 TRP B 414 HIS 0.007 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.23 (20511) covalent geometry : angle 0.64387 / 0.34 (27943) hydrogen bonds : bond 0.04954 / 3.31 ( 804) hydrogen bonds : angle 4.55590 / 3.11 ( 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 : 0.809 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: 0.7113 (ptm) cc_final: 0.6858 (ppp) REVERT: B 204 MET cc_start: 0.7500 (ttt) cc_final: 0.7122 (tpt) REVERT: B 718 MET cc_start: 0.9532 (ptp) cc_final: 0.9310 (ptt) REVERT: A 61 MET cc_start: 0.6551 (ptm) cc_final: 0.6239 (ppp) REVERT: A 135 MET cc_start: 0.2129 (tpt) cc_final: 0.1832 (tmm) REVERT: A 189 MET cc_start: 0.4375 (tpt) cc_final: 0.4109 (tpt) REVERT: A 204 MET cc_start: 0.7295 (mmm) cc_final: 0.6982 (tpt) REVERT: A 718 MET cc_start: 0.8865 (ptp) cc_final: 0.8558 (ptt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1446 time to fit residues: 19.2152 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 : 0.633 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 230 optimal weight: 0.0970 chunk 79 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN B 746 GLN B 938 GLN A 91 ASN A 171 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.021615 restraints weight = 330822.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.022172 restraints weight = 221274.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.022530 restraints weight = 165253.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022769 restraints weight = 135278.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.022981 restraints weight = 117022.007| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20511 Z= 0.197 Angle : 0.618 12.763 27943 Z= 0.330 Chirality : 0.041 0.245 3081 Planarity : 0.004 0.058 3339 Dihedral : 16.530 145.364 3141 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -0.68 (0.18), residues: 2307 helix: 1.07 (0.17), residues: 958 sheet: -1.47 (0.31), residues: 317 loop : -1.60 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1020 TYR 0.026 0.002 TYR A 830 PHE 0.023 0.002 PHE B 417 TRP 0.029 0.002 TRP B 931 HIS 0.005 0.001 HIS B 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (20511) covalent geometry : angle 0.61827 / 0.33 (27943) hydrogen bonds : bond 0.03762 / 2.49 ( 804) hydrogen bonds : angle 4.65442 / 3.17 ( 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 83 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.765 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: 0.7113 (ptm) cc_final: 0.6891 (ppp) REVERT: B 204 MET cc_start: 0.7739 (ttt) cc_final: 0.7390 (tpt) REVERT: B 718 MET cc_start: 0.9463 (ptp) cc_final: 0.9226 (ptt) REVERT: B 766 MET cc_start: 0.9601 (mpp) cc_final: 0.9390 (mpp) REVERT: B 943 MET cc_start: 0.8969 (tpt) cc_final: 0.8671 (tpt) REVERT: A 189 MET cc_start: 0.4380 (tpt) cc_final: 0.4029 (tpt) REVERT: A 769 ILE cc_start: 0.9688 (mt) cc_final: 0.9437 (tp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1531 time to fit residues: 20.3490 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 : 0.691 ------------------------------------------------------------------------------- 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: 4.9990 chunk 210 optimal weight: 0.1980 chunk 187 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 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 = 0.3183 r_free = 0.3183 target = 0.037094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.021750 restraints weight = 327403.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.022324 restraints weight = 216986.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.022724 restraints weight = 163399.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.022973 restraints weight = 131821.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.023189 restraints weight = 114043.865| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20511 Z= 0.138 Angle : 0.547 12.722 27943 Z= 0.292 Chirality : 0.040 0.218 3081 Planarity : 0.004 0.055 3339 Dihedral : 16.510 145.164 3141 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -0.61 (0.18), residues: 2307 helix: 1.14 (0.17), residues: 964 sheet: -1.50 (0.30), residues: 317 loop : -1.55 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 672 TYR 0.020 0.001 TYR A 830 PHE 0.021 0.001 PHE A 668 TRP 0.022 0.002 TRP B 931 HIS 0.003 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (20511) covalent geometry : angle 0.54721 / 0.29 (27943) hydrogen bonds : bond 0.03547 / 2.34 ( 804) hydrogen bonds : angle 4.58943 / 3.14 ( 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 82 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.770 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: 0.7008 (ptm) cc_final: 0.6778 (ppp) REVERT: B 204 MET cc_start: 0.7708 (ttt) cc_final: 0.7347 (tpt) REVERT: B 766 MET cc_start: 0.9587 (mpp) cc_final: 0.9358 (mpp) REVERT: A 61 MET cc_start: 0.6529 (ptm) cc_final: 0.6202 (ppp) REVERT: A 189 MET cc_start: 0.4718 (tpt) cc_final: 0.4487 (tpt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1491 time to fit residues: 20.1653 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 : 0.590 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 30.0000 chunk 182 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 118 optimal weight: 40.0000 chunk 2 optimal weight: 40.0000 chunk 64 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.036827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.021511 restraints weight = 331293.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.022100 restraints weight = 219539.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.022509 restraints weight = 164931.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.022771 restraints weight = 132811.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.022971 restraints weight = 115018.279| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20511 Z= 0.148 Angle : 0.557 12.397 27943 Z= 0.298 Chirality : 0.040 0.212 3081 Planarity : 0.003 0.042 3339 Dihedral : 16.521 145.152 3141 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.57 (0.18), residues: 2307 helix: 1.16 (0.17), residues: 963 sheet: -1.52 (0.31), residues: 311 loop : -1.51 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 672 TYR 0.020 0.001 TYR A 830 PHE 0.016 0.002 PHE B 807 TRP 0.024 0.002 TRP B 931 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (20511) covalent geometry : angle 0.55740 / 0.30 (27943) hydrogen bonds : bond 0.03563 / 2.37 ( 804) hydrogen bonds : angle 4.57485 / 3.13 ( 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 81 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.778 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: B 135 MET cc_start: 0.6987 (ptm) cc_final: 0.6752 (ppp) REVERT: B 204 MET cc_start: 0.7681 (ttt) cc_final: 0.7312 (tpt) REVERT: B 718 MET cc_start: 0.9431 (ptp) cc_final: 0.9161 (ptp) REVERT: B 766 MET cc_start: 0.9588 (mpp) cc_final: 0.9373 (mpp) REVERT: B 809 MET cc_start: 0.9506 (tpt) cc_final: 0.9285 (mmm) REVERT: A 61 MET cc_start: 0.6507 (ptm) cc_final: 0.6176 (ppp) REVERT: A 189 MET cc_start: 0.4786 (tpt) cc_final: 0.4536 (tpt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1435 time to fit residues: 18.8154 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 : 0.669 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 50.0000 chunk 203 optimal weight: 5.9990 chunk 234 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3171 r_free = 0.3171 target = 0.036649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.021503 restraints weight = 333680.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.022047 restraints weight = 219838.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.022441 restraints weight = 166426.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.022695 restraints weight = 134470.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.022906 restraints weight = 115893.829| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20511 Z= 0.159 Angle : 0.577 14.875 27943 Z= 0.309 Chirality : 0.040 0.219 3081 Planarity : 0.004 0.043 3339 Dihedral : 16.561 145.513 3141 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % 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: -0.56 (0.18), residues: 2307 helix: 1.15 (0.17), residues: 962 sheet: -1.52 (0.31), residues: 306 loop : -1.48 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 672 TYR 0.020 0.001 TYR A 830 PHE 0.018 0.002 PHE A 573 TRP 0.026 0.002 TRP B 931 HIS 0.004 0.001 HIS A 961 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (20511) covalent geometry : angle 0.57749 / 0.31 (27943) hydrogen bonds : bond 0.03707 / 2.48 ( 804) hydrogen bonds : angle 4.62182 / 3.17 ( 2210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4468.81 seconds wall clock time: 77 minutes 41.19 seconds (4661.19 seconds total)