Starting phenix.real_space_refine on Thu Mar 5 07:52:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy7_11553/03_2026/6zy7_11553.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy7_11553/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zy7_11553/03_2026/6zy7_11553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy7_11553/03_2026/6zy7_11553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy7_11553/03_2026/6zy7_11553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy7_11553/03_2026/6zy7_11553.map" } 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19979 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 9310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9310 Classifications: {'peptide': 1160} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 1114} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 9305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9305 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 1113} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.55, per 1000 atoms: 0.23 Number of scatterers: 19979 At special positions: 0 Unit cell: (119.053, 116.039, 197.417, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 62 15.00 O 3881 8.00 N 3417 7.00 C 12527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.44 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: 4.55 Time building geometry restraints manager: 2.28 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: 26567 2.17 - 4.33: 1330 4.33 - 6.50: 38 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: 12007 28.12 - 56.23: 348 56.23 - 84.35: 56 84.35 - 112.47: 4 112.47 - 140.58: 2 Dihedral angle restraints: 12417 sinusoidal: 5666 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 12414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1877 0.057 - 0.114: 770 0.114 - 0.171: 325 0.171 - 0.228: 93 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.020 Find NCS groups from input model: 0.520 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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= 0.663 Angle : 1.010 10.829 27943 Z= 0.737 Chirality : 0.076 0.285 3081 Planarity : 0.006 0.038 3339 Dihedral : 12.600 140.584 8063 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 covalent geometry : bond 0.00937 (20511) covalent geometry : angle 1.00972 (27943) hydrogen bonds : bond 0.21858 ( 804) hydrogen bonds : angle 6.85707 ( 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 : 0.711 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: 0.1964 time to fit residues: 44.9168 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 : 0.719 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 315 ASN B 498 HIS B 558 HIS B 634 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 498 HIS A 558 HIS A 634 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.041623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025018 restraints weight = 310985.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.025737 restraints weight = 205597.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026194 restraints weight = 152833.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026505 restraints weight = 123750.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.026800 restraints weight = 106380.887| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20511 Z= 0.132 Angle : 0.500 5.529 27943 Z= 0.272 Chirality : 0.038 0.269 3081 Planarity : 0.004 0.047 3339 Dihedral : 15.691 138.525 3335 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -1.07 (0.18), residues: 2307 helix: 1.05 (0.18), residues: 921 sheet: -1.68 (0.28), residues: 363 loop : -2.03 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.015 0.001 TYR A 830 PHE 0.014 0.001 PHE A 85 TRP 0.024 0.002 TRP B1090 HIS 0.004 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00271 (20511) covalent geometry : angle 0.50035 (27943) hydrogen bonds : bond 0.04093 ( 804) hydrogen bonds : angle 4.62186 ( 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 : 0.745 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: B 718 MET cc_start: 0.8933 (ptm) cc_final: 0.8726 (ptt) REVERT: B 943 MET cc_start: 0.9029 (tpt) cc_final: 0.8810 (tpt) REVERT: A 61 MET cc_start: 0.6388 (ptm) cc_final: 0.6170 (pmm) REVERT: A 669 MET cc_start: 0.9612 (ppp) cc_final: 0.9407 (ppp) REVERT: A 718 MET cc_start: 0.8727 (ptp) cc_final: 0.8312 (ptt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1807 time to fit residues: 28.6480 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 : 0.761 ------------------------------------------------------------------------------- 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: 8.9990 chunk 135 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 overall best weight: 5.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN B 567 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS A 508 ASN A 567 HIS A 667 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.038156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022400 restraints weight = 331494.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.022967 restraints weight = 225494.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.023341 restraints weight = 170843.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.023638 restraints weight = 140439.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.023776 restraints weight = 121168.159| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 20511 Z= 0.211 Angle : 0.592 7.497 27943 Z= 0.314 Chirality : 0.040 0.227 3081 Planarity : 0.004 0.047 3339 Dihedral : 15.941 142.577 3335 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.05 % Allowed : 0.98 % Favored : 98.97 % 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: 0.96 (0.17), residues: 954 sheet: -1.80 (0.28), residues: 386 loop : -1.83 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 672 TYR 0.022 0.002 TYR A 830 PHE 0.012 0.002 PHE B 589 TRP 0.022 0.002 TRP A1090 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00440 (20511) covalent geometry : angle 0.59248 (27943) hydrogen bonds : bond 0.04174 ( 804) hydrogen bonds : angle 4.57992 ( 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 93 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.756 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: 0.6959 (ptm) cc_final: 0.6603 (ppp) REVERT: B 765 MET cc_start: 0.9707 (ptp) cc_final: 0.9486 (mmm) REVERT: A 61 MET cc_start: 0.6559 (ptm) cc_final: 0.6325 (pmm) REVERT: A 718 MET cc_start: 0.8749 (ptp) cc_final: 0.8374 (ptt) REVERT: A 769 ILE cc_start: 0.9725 (mt) cc_final: 0.9493 (tp) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1658 time to fit residues: 23.9134 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 : 0.722 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 151 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 149 optimal weight: 50.0000 chunk 168 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 393 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.039436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.023320 restraints weight = 323072.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.023961 restraints weight = 211890.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.024387 restraints weight = 157742.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.024722 restraints weight = 127524.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.024978 restraints weight = 108949.792| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20511 Z= 0.090 Angle : 0.453 6.794 27943 Z= 0.242 Chirality : 0.038 0.180 3081 Planarity : 0.003 0.047 3339 Dihedral : 15.836 142.194 3335 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -0.61 (0.18), residues: 2307 helix: 1.36 (0.18), residues: 947 sheet: -1.51 (0.30), residues: 338 loop : -1.74 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 870 TYR 0.012 0.001 TYR A 830 PHE 0.010 0.001 PHE A 706 TRP 0.012 0.001 TRP A 414 HIS 0.002 0.000 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00188 (20511) covalent geometry : angle 0.45288 (27943) hydrogen bonds : bond 0.02759 ( 804) hydrogen bonds : angle 4.24055 ( 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 93 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.818 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: 0.6972 (ptm) cc_final: 0.6593 (ppp) REVERT: B 768 ILE cc_start: 0.9601 (mt) cc_final: 0.9191 (mm) REVERT: B 809 MET cc_start: 0.9442 (tpt) cc_final: 0.9201 (tpt) REVERT: A 61 MET cc_start: 0.6480 (ptm) cc_final: 0.6266 (pmm) REVERT: A 537 MET cc_start: 0.7449 (tpp) cc_final: 0.7092 (tpp) REVERT: A 669 MET cc_start: 0.9649 (ppp) cc_final: 0.9442 (ppp) REVERT: A 718 MET cc_start: 0.8843 (ptp) cc_final: 0.8435 (ptt) REVERT: A 769 ILE cc_start: 0.9675 (mt) cc_final: 0.9384 (tp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1645 time to fit residues: 23.5212 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 : 0.724 ------------------------------------------------------------------------------- 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: 10.0000 chunk 232 optimal weight: 0.9990 chunk 146 optimal weight: 50.0000 chunk 220 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 HIS B 746 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 197 ASN ** A 746 GLN ** 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 = 0.3188 r_free = 0.3188 target = 0.037080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021761 restraints weight = 328274.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.022324 restraints weight = 218675.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.022734 restraints weight = 165413.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.022977 restraints weight = 133145.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.023195 restraints weight = 114481.865| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20511 Z= 0.189 Angle : 0.550 5.331 27943 Z= 0.295 Chirality : 0.040 0.247 3081 Planarity : 0.004 0.044 3339 Dihedral : 16.044 144.608 3335 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.05 % Allowed : 0.83 % 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: -0.64 (0.18), residues: 2307 helix: 1.18 (0.17), residues: 948 sheet: -1.49 (0.31), residues: 311 loop : -1.61 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1160 TYR 0.023 0.001 TYR A 830 PHE 0.026 0.002 PHE B 417 TRP 0.020 0.002 TRP B 931 HIS 0.004 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00389 (20511) covalent geometry : angle 0.55018 (27943) hydrogen bonds : bond 0.04000 ( 804) hydrogen bonds : angle 4.44053 ( 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 88 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.824 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: B 135 MET cc_start: 0.7198 (ptm) cc_final: 0.6899 (ppp) REVERT: B 943 MET cc_start: 0.8968 (tpt) cc_final: 0.8767 (tpt) REVERT: A 135 MET cc_start: 0.2122 (tpt) cc_final: 0.1914 (tmm) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1658 time to fit residues: 22.8902 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 : 0.732 ------------------------------------------------------------------------------- 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: 50.0000 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 204 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 GLN A 91 ASN A 171 ASN A 370 ASN A 445 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.021001 restraints weight = 329963.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021554 restraints weight = 219226.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.021925 restraints weight = 165519.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.022188 restraints weight = 134765.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.022418 restraints weight = 116099.620| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20511 Z= 0.184 Angle : 0.557 8.914 27943 Z= 0.299 Chirality : 0.039 0.190 3081 Planarity : 0.004 0.046 3339 Dihedral : 16.378 147.546 3335 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2307 helix: 1.00 (0.17), residues: 959 sheet: -1.59 (0.30), residues: 314 loop : -1.56 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 635 TYR 0.023 0.002 TYR A 830 PHE 0.016 0.002 PHE B 807 TRP 0.025 0.002 TRP B 931 HIS 0.004 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00377 (20511) covalent geometry : angle 0.55706 (27943) hydrogen bonds : bond 0.03748 ( 804) hydrogen bonds : angle 4.58086 ( 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 87 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.694 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: 0.7014 (ptm) cc_final: 0.6621 (ppp) REVERT: B 943 MET cc_start: 0.9057 (tpt) cc_final: 0.8788 (tpt) REVERT: A 189 MET cc_start: 0.4989 (tpt) cc_final: 0.4702 (tpt) REVERT: A 537 MET cc_start: 0.7092 (tpp) cc_final: 0.6873 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1625 time to fit residues: 22.0573 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 : 0.731 ------------------------------------------------------------------------------- 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: 3.9990 chunk 202 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 155 optimal weight: 0.0470 overall best weight: 5.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN A 558 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.035257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.020407 restraints weight = 338522.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.020978 restraints weight = 226448.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.021318 restraints weight = 169270.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.021573 restraints weight = 137998.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021698 restraints weight = 119426.332| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5613 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= 0.208 Angle : 0.597 7.945 27943 Z= 0.319 Chirality : 0.040 0.220 3081 Planarity : 0.004 0.047 3339 Dihedral : 16.588 149.763 3335 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 2307 helix: 0.83 (0.17), residues: 956 sheet: -1.59 (0.30), residues: 323 loop : -1.48 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 672 TYR 0.024 0.002 TYR A 830 PHE 0.018 0.002 PHE A 731 TRP 0.030 0.002 TRP B 931 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00429 (20511) covalent geometry : angle 0.59747 (27943) hydrogen bonds : bond 0.04334 ( 804) hydrogen bonds : angle 4.81620 ( 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 83 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.762 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 381 MET cc_start: 0.5162 (tpp) cc_final: 0.4947 (tpt) REVERT: B 669 MET cc_start: 0.9772 (ppp) cc_final: 0.9563 (ppp) REVERT: A 135 MET cc_start: 0.1935 (tpt) cc_final: 0.1658 (tmm) REVERT: A 189 MET cc_start: 0.4684 (tpt) cc_final: 0.4356 (tpt) REVERT: A 204 MET cc_start: 0.7408 (tpt) cc_final: 0.7165 (tpt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1488 time to fit residues: 19.9400 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 : 0.695 ------------------------------------------------------------------------------- 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: 6.9990 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 230 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 218 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 961 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.035860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.020788 restraints weight = 333095.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.021366 restraints weight = 219821.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.021719 restraints weight = 162692.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.021985 restraints weight = 132187.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.022122 restraints weight = 113087.240| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20511 Z= 0.139 Angle : 0.523 8.067 27943 Z= 0.278 Chirality : 0.039 0.191 3081 Planarity : 0.003 0.040 3339 Dihedral : 16.479 149.278 3335 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2307 helix: 1.03 (0.17), residues: 968 sheet: -1.53 (0.31), residues: 314 loop : -1.45 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.016 0.001 TYR A 830 PHE 0.030 0.001 PHE A 573 TRP 0.026 0.002 TRP B 931 HIS 0.004 0.001 HIS A 961 Details of bonding type rmsd covalent geometry : bond 0.00290 (20511) covalent geometry : angle 0.52324 (27943) hydrogen bonds : bond 0.03376 ( 804) hydrogen bonds : angle 4.64072 ( 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 85 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.742 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: 0.6570 (ptm) cc_final: 0.6182 (ppp) REVERT: B 766 MET cc_start: 0.9585 (mpp) cc_final: 0.9374 (mpp) REVERT: B 1131 MET cc_start: 0.8068 (mpp) cc_final: 0.7855 (mpp) REVERT: A 189 MET cc_start: 0.5471 (tpt) cc_final: 0.5189 (tpt) REVERT: A 718 MET cc_start: 0.7910 (ptt) cc_final: 0.7591 (ptt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1510 time to fit residues: 20.6977 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 : 0.747 ------------------------------------------------------------------------------- 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: 7.9990 chunk 210 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 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: 30.0000 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3128 r_free = 0.3128 target = 0.035291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.020412 restraints weight = 336656.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.021009 restraints weight = 223201.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.021376 restraints weight = 164198.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.021622 restraints weight = 132512.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021749 restraints weight = 114336.015| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20511 Z= 0.159 Angle : 0.548 7.759 27943 Z= 0.290 Chirality : 0.039 0.198 3081 Planarity : 0.003 0.041 3339 Dihedral : 16.471 149.311 3335 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2307 helix: 1.02 (0.17), residues: 967 sheet: -1.45 (0.31), residues: 315 loop : -1.45 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 487 TYR 0.017 0.002 TYR A 830 PHE 0.019 0.002 PHE A 573 TRP 0.033 0.002 TRP B 931 HIS 0.004 0.001 HIS B 961 Details of bonding type rmsd covalent geometry : bond 0.00332 (20511) covalent geometry : angle 0.54803 (27943) hydrogen bonds : bond 0.03685 ( 804) hydrogen bonds : angle 4.63931 ( 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 81 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.763 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: 0.6252 (ptm) cc_final: 0.5861 (ppp) REVERT: A 135 MET cc_start: 0.2136 (tpt) cc_final: 0.1800 (tmm) REVERT: A 189 MET cc_start: 0.5432 (tpt) cc_final: 0.5135 (tpt) REVERT: A 204 MET cc_start: 0.7348 (tpt) cc_final: 0.7110 (tpt) REVERT: A 718 MET cc_start: 0.7782 (ptt) cc_final: 0.7488 (ptt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1444 time to fit residues: 19.3958 Evaluate side-chains 74 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 2 optimal weight: 50.0000 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 292 GLN B 917 ASN ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.035248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.022265 restraints weight = 330458.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.022672 restraints weight = 214171.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.022940 restraints weight = 158018.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.023063 restraints weight = 127144.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.023228 restraints weight = 111687.591| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20511 Z= 0.180 Angle : 0.583 8.275 27943 Z= 0.309 Chirality : 0.040 0.199 3081 Planarity : 0.004 0.041 3339 Dihedral : 16.671 150.674 3335 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2307 helix: 0.87 (0.17), residues: 974 sheet: -1.54 (0.31), residues: 312 loop : -1.50 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 487 TYR 0.019 0.002 TYR A 892 PHE 0.019 0.002 PHE B 731 TRP 0.033 0.002 TRP B 931 HIS 0.007 0.001 HIS B 961 Details of bonding type rmsd covalent geometry : bond 0.00374 (20511) covalent geometry : angle 0.58321 (27943) hydrogen bonds : bond 0.03907 ( 804) hydrogen bonds : angle 4.81284 ( 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 79 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 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: B 135 MET cc_start: 0.6028 (ptm) cc_final: 0.5642 (ppp) REVERT: B 669 MET cc_start: 0.9870 (ppp) cc_final: 0.9661 (ppp) REVERT: B 765 MET cc_start: 0.9681 (mmp) cc_final: 0.9444 (mmm) REVERT: B 766 MET cc_start: 0.9723 (mpp) cc_final: 0.9506 (mpp) REVERT: B 809 MET cc_start: 0.9314 (tpt) cc_final: 0.9101 (tpt) REVERT: B 1131 MET cc_start: 0.9573 (mpp) cc_final: 0.9212 (mpp) REVERT: A 189 MET cc_start: 0.5664 (tpt) cc_final: 0.5318 (tpt) REVERT: A 539 MET cc_start: 0.9349 (mmm) cc_final: 0.8276 (mmm) REVERT: A 718 MET cc_start: 0.8405 (ptt) cc_final: 0.7965 (ptt) REVERT: A 847 MET cc_start: 0.9686 (mmp) cc_final: 0.9272 (tmm) REVERT: A 972 MET cc_start: 0.9209 (pmm) cc_final: 0.8935 (pmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1378 time to fit residues: 18.2908 Evaluate side-chains 73 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 29 optimal weight: 40.0000 chunk 91 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 153 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 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 = 0.3118 r_free = 0.3118 target = 0.034975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.020124 restraints weight = 340296.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.020608 restraints weight = 231769.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.021006 restraints weight = 172317.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.021304 restraints weight = 136946.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.021447 restraints weight = 115270.041| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20511 Z= 0.146 Angle : 0.540 7.603 27943 Z= 0.286 Chirality : 0.039 0.187 3081 Planarity : 0.003 0.042 3339 Dihedral : 16.600 149.882 3335 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2307 helix: 1.05 (0.17), residues: 963 sheet: -1.58 (0.30), residues: 319 loop : -1.36 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 487 TYR 0.015 0.001 TYR B 64 PHE 0.027 0.002 PHE B 417 TRP 0.033 0.002 TRP B 931 HIS 0.005 0.001 HIS B 759 Details of bonding type rmsd covalent geometry : bond 0.00306 (20511) covalent geometry : angle 0.54026 (27943) hydrogen bonds : bond 0.03425 ( 804) hydrogen bonds : angle 4.71601 ( 2210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.09 seconds wall clock time: 84 minutes 23.49 seconds (5063.49 seconds total)