Starting phenix.real_space_refine on Sat Sep 28 21:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/09_2024/6zy7_11553.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/09_2024/6zy7_11553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/09_2024/6zy7_11553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/09_2024/6zy7_11553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/09_2024/6zy7_11553.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/09_2024/6zy7_11553.cif" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.11, per 1000 atoms: 0.56 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: 5.23 Conformation dependent library (CDL) restraints added in 2.5 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: 6.52 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: 8.23 Time building geometry restraints manager: 5.98 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 1215 or resid 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: 0.750 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: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 49.380 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.080 ------------------------------------------------------------------------------- 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= 0.597 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 : 6.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP B1167 HIS 0.004 0.001 HIS A 986 PHE 0.010 0.001 PHE B 417 TYR 0.022 0.002 TYR A 830 ARG 0.006 0.001 ARG B 804 *********************** 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 fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.314 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: 0.4240 (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: 0.9487 (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: 0.9445 (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: 0.9242 (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: 0.4116 time to fit residues: 94.1313 Evaluate side-chains 103 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 0.0170 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20511 Z= 0.169 Angle : 0.500 6.822 27943 Z= 0.272 Chirality : 0.039 0.267 3081 Planarity : 0.004 0.047 3339 Dihedral : 15.694 138.420 3335 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2307 helix: 1.02 (0.18), residues: 928 sheet: -1.67 (0.28), residues: 363 loop : -2.05 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1090 HIS 0.003 0.001 HIS A 759 PHE 0.016 0.001 PHE A 85 TYR 0.017 0.001 TYR A 830 ARG 0.003 0.000 ARG B 241 *********************** 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 109 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.493 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 102 MET cc_start: -0.0753 (tmm) cc_final: -0.0953 (tmm) REVERT: B 537 MET cc_start: 0.9109 (tpt) cc_final: 0.8870 (tpp) REVERT: B 718 MET cc_start: 0.9296 (ptm) cc_final: 0.8959 (ptt) REVERT: B 761 GLU cc_start: 0.9388 (pm20) cc_final: 0.9167 (pm20) REVERT: B 805 TYR cc_start: 0.8772 (m-10) cc_final: 0.8010 (m-10) REVERT: B 809 MET cc_start: 0.9411 (ttp) cc_final: 0.8874 (mmm) REVERT: B 943 MET cc_start: 0.9608 (tpt) cc_final: 0.9380 (tpt) REVERT: B 972 MET cc_start: 0.9311 (mpp) cc_final: 0.8577 (mpp) REVERT: A 61 MET cc_start: 0.5359 (ptm) cc_final: 0.5099 (pmm) REVERT: A 102 MET cc_start: 0.6651 (tmm) cc_final: 0.6369 (tmm) REVERT: A 459 LEU cc_start: 0.9615 (mt) cc_final: 0.9391 (mm) REVERT: A 539 MET cc_start: 0.9422 (ptm) cc_final: 0.9111 (ppp) REVERT: A 718 MET cc_start: 0.9001 (ptp) cc_final: 0.8562 (ptt) REVERT: A 972 MET cc_start: 0.9184 (pmm) cc_final: 0.8659 (pmm) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.4008 time to fit residues: 65.4240 Evaluate side-chains 90 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 145 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS A 91 ASN A 508 ASN A 567 HIS A 667 ASN A 700 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN A 824 HIS A1050 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 20511 Z= 0.372 Angle : 0.746 10.978 27943 Z= 0.392 Chirality : 0.044 0.311 3081 Planarity : 0.005 0.047 3339 Dihedral : 16.314 144.777 3335 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.05 % Allowed : 1.03 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2307 helix: 0.43 (0.16), residues: 961 sheet: -1.59 (0.30), residues: 316 loop : -2.02 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B1036 HIS 0.009 0.002 HIS B 605 PHE 0.019 0.003 PHE B 807 TYR 0.034 0.002 TYR A 830 ARG 0.006 0.001 ARG B 929 *********************** 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 fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.5560 (ptm) cc_final: 0.5096 (ppp) REVERT: B 204 MET cc_start: 0.5583 (ttt) cc_final: 0.4771 (tpt) REVERT: B 228 MET cc_start: 0.8908 (ptp) cc_final: 0.8683 (pmm) REVERT: B 809 MET cc_start: 0.9494 (ttp) cc_final: 0.9259 (mmm) REVERT: B 943 MET cc_start: 0.9668 (tpt) cc_final: 0.9350 (tpp) REVERT: B 972 MET cc_start: 0.9650 (mpp) cc_final: 0.9094 (mpp) REVERT: B 1131 MET cc_start: 0.8697 (pmm) cc_final: 0.8472 (pmm) REVERT: A 198 MET cc_start: 0.7949 (mtt) cc_final: 0.7611 (mmt) REVERT: A 718 MET cc_start: 0.9086 (ptp) cc_final: 0.8757 (ptt) REVERT: A 809 MET cc_start: 0.9465 (ttp) cc_final: 0.9173 (ttp) REVERT: A 972 MET cc_start: 0.9233 (pmm) cc_final: 0.8735 (pmm) REVERT: A 1131 MET cc_start: 0.9368 (ppp) cc_final: 0.9064 (mpp) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.3758 time to fit residues: 54.0616 Evaluate side-chains 78 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 0.0270 chunk 110 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN B 150 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20511 Z= 0.127 Angle : 0.471 7.387 27943 Z= 0.252 Chirality : 0.038 0.194 3081 Planarity : 0.003 0.047 3339 Dihedral : 16.026 144.217 3335 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2307 helix: 1.18 (0.17), residues: 953 sheet: -1.64 (0.30), residues: 335 loop : -1.77 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 414 HIS 0.003 0.001 HIS B 634 PHE 0.019 0.001 PHE B 417 TYR 0.014 0.001 TYR B1030 ARG 0.003 0.000 ARG A 200 *********************** 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 fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.196 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: 0.5418 (ptm) cc_final: 0.4990 (ppp) REVERT: B 537 MET cc_start: 0.9268 (tpp) cc_final: 0.8950 (tpp) REVERT: B 718 MET cc_start: 0.9252 (ptm) cc_final: 0.9001 (ptt) REVERT: B 943 MET cc_start: 0.9684 (tpt) cc_final: 0.9404 (tpp) REVERT: B 972 MET cc_start: 0.9482 (mpp) cc_final: 0.8609 (mpp) REVERT: A 189 MET cc_start: 0.4451 (tpt) cc_final: 0.4230 (tpt) REVERT: A 198 MET cc_start: 0.7889 (mtt) cc_final: 0.7518 (mmt) REVERT: A 204 MET cc_start: 0.6335 (tpp) cc_final: 0.6041 (mmt) REVERT: A 718 MET cc_start: 0.9176 (ptp) cc_final: 0.8755 (ptt) REVERT: A 766 MET cc_start: 0.9680 (tpp) cc_final: 0.9466 (tpp) REVERT: A 769 ILE cc_start: 0.9871 (mt) cc_final: 0.9628 (tp) REVERT: A 809 MET cc_start: 0.9433 (ttp) cc_final: 0.9079 (ttp) REVERT: A 972 MET cc_start: 0.9263 (pmm) cc_final: 0.8765 (pmm) REVERT: A 1131 MET cc_start: 0.9193 (ppp) cc_final: 0.8760 (mpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3197 time to fit residues: 47.3130 Evaluate side-chains 82 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.1980 chunk 93 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 157 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 115 optimal weight: 30.0000 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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** B 938 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20511 Z= 0.160 Angle : 0.471 5.218 27943 Z= 0.253 Chirality : 0.038 0.169 3081 Planarity : 0.003 0.041 3339 Dihedral : 15.970 144.253 3335 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2307 helix: 1.35 (0.17), residues: 946 sheet: -1.58 (0.31), residues: 315 loop : -1.61 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 931 HIS 0.005 0.001 HIS B 759 PHE 0.014 0.001 PHE B 417 TYR 0.013 0.001 TYR A 830 ARG 0.002 0.000 ARG B1020 *********************** 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 86 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.5659 (ptm) cc_final: 0.5247 (ppp) REVERT: B 204 MET cc_start: 0.6376 (ttt) cc_final: 0.5693 (tpt) REVERT: B 381 MET cc_start: 0.3894 (tpp) cc_final: 0.3630 (tpt) REVERT: B 537 MET cc_start: 0.9128 (tpp) cc_final: 0.8846 (tpp) REVERT: B 765 MET cc_start: 0.9467 (ptp) cc_final: 0.9207 (mmm) REVERT: B 972 MET cc_start: 0.9530 (mpp) cc_final: 0.8946 (mpp) REVERT: A 189 MET cc_start: 0.4399 (tpt) cc_final: 0.4140 (tpt) REVERT: A 198 MET cc_start: 0.7841 (mtt) cc_final: 0.7488 (mmt) REVERT: A 718 MET cc_start: 0.9217 (ptp) cc_final: 0.8782 (ptt) REVERT: A 809 MET cc_start: 0.9440 (ttp) cc_final: 0.9120 (ttp) REVERT: A 972 MET cc_start: 0.9245 (pmm) cc_final: 0.8666 (pmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3533 time to fit residues: 48.2524 Evaluate side-chains 76 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.5980 chunk 204 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 133 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 6.7188 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 370 ASN A 393 GLN A 700 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20511 Z= 0.329 Angle : 0.670 8.847 27943 Z= 0.356 Chirality : 0.042 0.293 3081 Planarity : 0.004 0.048 3339 Dihedral : 16.599 149.185 3335 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2307 helix: 0.77 (0.17), residues: 952 sheet: -1.69 (0.30), residues: 317 loop : -1.61 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 931 HIS 0.008 0.002 HIS B 290 PHE 0.019 0.002 PHE B 807 TYR 0.033 0.002 TYR A 830 ARG 0.007 0.001 ARG A1160 *********************** 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 83 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.256 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: 0.5357 (ptm) cc_final: 0.4893 (ppp) REVERT: B 204 MET cc_start: 0.6995 (ttt) cc_final: 0.6403 (tpt) REVERT: B 381 MET cc_start: 0.4278 (tpp) cc_final: 0.4021 (tpt) REVERT: B 537 MET cc_start: 0.8918 (tpp) cc_final: 0.8623 (tpp) REVERT: B 669 MET cc_start: 0.9615 (ppp) cc_final: 0.9386 (ppp) REVERT: B 943 MET cc_start: 0.9548 (tpt) cc_final: 0.9204 (tpp) REVERT: B 972 MET cc_start: 0.9590 (mpp) cc_final: 0.9038 (mpp) REVERT: A 189 MET cc_start: 0.5131 (tpt) cc_final: 0.4848 (tpt) REVERT: A 198 MET cc_start: 0.8264 (mtt) cc_final: 0.7976 (tpp) REVERT: A 539 MET cc_start: 0.9452 (ppp) cc_final: 0.9246 (ppp) REVERT: A 669 MET cc_start: 0.9409 (ppp) cc_final: 0.9168 (ppp) REVERT: A 718 MET cc_start: 0.9155 (ptp) cc_final: 0.8929 (ptm) REVERT: A 972 MET cc_start: 0.9236 (pmm) cc_final: 0.8725 (pmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3246 time to fit residues: 43.6692 Evaluate side-chains 75 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 chunk 226 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 558 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.5208 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= 0.160 Angle : 0.503 8.186 27943 Z= 0.268 Chirality : 0.039 0.173 3081 Planarity : 0.003 0.036 3339 Dihedral : 16.419 148.486 3335 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2307 helix: 1.17 (0.17), residues: 946 sheet: -1.59 (0.31), residues: 313 loop : -1.44 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 931 HIS 0.003 0.001 HIS B 759 PHE 0.016 0.001 PHE A 731 TYR 0.015 0.001 TYR A 830 ARG 0.005 0.000 ARG A 740 *********************** 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 85 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.5074 (ptm) cc_final: 0.4607 (ppp) REVERT: B 204 MET cc_start: 0.6905 (ttt) cc_final: 0.6306 (tpt) REVERT: B 381 MET cc_start: 0.4186 (tpp) cc_final: 0.3914 (tpt) REVERT: B 537 MET cc_start: 0.8936 (tpp) cc_final: 0.8637 (tpp) REVERT: B 809 MET cc_start: 0.9558 (tpt) cc_final: 0.9354 (mmm) REVERT: B 943 MET cc_start: 0.9537 (tpt) cc_final: 0.9115 (tpt) REVERT: B 972 MET cc_start: 0.9530 (mpp) cc_final: 0.8800 (mpp) REVERT: B 1131 MET cc_start: 0.9420 (mpp) cc_final: 0.9060 (mpp) REVERT: A 189 MET cc_start: 0.5112 (tpt) cc_final: 0.4748 (tpt) REVERT: A 198 MET cc_start: 0.8412 (mtt) cc_final: 0.8141 (tpp) REVERT: A 537 MET cc_start: 0.7466 (tpp) cc_final: 0.7233 (tpp) REVERT: A 669 MET cc_start: 0.9307 (ppp) cc_final: 0.9088 (ppp) REVERT: A 718 MET cc_start: 0.9138 (ptp) cc_final: 0.8916 (ptm) REVERT: A 972 MET cc_start: 0.9204 (pmm) cc_final: 0.8677 (pmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3238 time to fit residues: 44.6289 Evaluate side-chains 75 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 746 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20511 Z= 0.217 Angle : 0.549 7.921 27943 Z= 0.292 Chirality : 0.039 0.192 3081 Planarity : 0.003 0.036 3339 Dihedral : 16.453 148.777 3335 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2307 helix: 1.14 (0.17), residues: 939 sheet: -1.42 (0.31), residues: 303 loop : -1.46 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 931 HIS 0.007 0.001 HIS A 961 PHE 0.017 0.002 PHE B 807 TYR 0.018 0.002 TYR A 830 ARG 0.005 0.001 ARG B 675 *********************** 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 81 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.349 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: 0.5029 (ptm) cc_final: 0.4549 (ppp) REVERT: B 204 MET cc_start: 0.6881 (ttt) cc_final: 0.6252 (tpt) REVERT: B 381 MET cc_start: 0.4284 (tpp) cc_final: 0.4043 (tpt) REVERT: B 537 MET cc_start: 0.8934 (tpp) cc_final: 0.8650 (tpp) REVERT: B 669 MET cc_start: 0.9625 (ppp) cc_final: 0.9380 (ppp) REVERT: B 809 MET cc_start: 0.9331 (tpt) cc_final: 0.9094 (mmm) REVERT: B 847 MET cc_start: 0.9549 (mmp) cc_final: 0.9171 (tpp) REVERT: B 943 MET cc_start: 0.9626 (tpt) cc_final: 0.9315 (tpp) REVERT: B 972 MET cc_start: 0.9550 (mpp) cc_final: 0.8956 (mpp) REVERT: B 1131 MET cc_start: 0.9435 (mpp) cc_final: 0.9110 (mpp) REVERT: A 189 MET cc_start: 0.5496 (tpt) cc_final: 0.5153 (tpt) REVERT: A 198 MET cc_start: 0.8557 (mtt) cc_final: 0.8312 (tpp) REVERT: A 537 MET cc_start: 0.7517 (tpp) cc_final: 0.6567 (tpp) REVERT: A 539 MET cc_start: 0.9455 (ppp) cc_final: 0.9216 (pmm) REVERT: A 669 MET cc_start: 0.9400 (ppp) cc_final: 0.9164 (ppp) REVERT: A 972 MET cc_start: 0.9159 (pmm) cc_final: 0.8629 (pmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3478 time to fit residues: 46.2576 Evaluate side-chains 75 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 0.0980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20511 Z= 0.145 Angle : 0.492 9.118 27943 Z= 0.261 Chirality : 0.038 0.171 3081 Planarity : 0.003 0.037 3339 Dihedral : 16.328 147.931 3335 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2307 helix: 1.31 (0.17), residues: 956 sheet: -1.44 (0.31), residues: 316 loop : -1.39 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 931 HIS 0.003 0.001 HIS B 961 PHE 0.013 0.001 PHE B 731 TYR 0.014 0.001 TYR A1030 ARG 0.004 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.5006 (ptm) cc_final: 0.4533 (ppp) REVERT: B 204 MET cc_start: 0.6736 (ttt) cc_final: 0.6094 (tpt) REVERT: B 381 MET cc_start: 0.4258 (tpp) cc_final: 0.4032 (tpt) REVERT: B 537 MET cc_start: 0.8923 (tpp) cc_final: 0.8605 (tpp) REVERT: B 669 MET cc_start: 0.9625 (ppp) cc_final: 0.9383 (ppp) REVERT: B 809 MET cc_start: 0.9473 (tpt) cc_final: 0.9138 (mmm) REVERT: B 847 MET cc_start: 0.9510 (mmp) cc_final: 0.9102 (tpp) REVERT: B 943 MET cc_start: 0.9634 (tpt) cc_final: 0.9313 (tpp) REVERT: B 972 MET cc_start: 0.9539 (mpp) cc_final: 0.8829 (mpp) REVERT: B 1131 MET cc_start: 0.9432 (mpp) cc_final: 0.9123 (mpp) REVERT: A 189 MET cc_start: 0.5413 (tpt) cc_final: 0.5114 (tpt) REVERT: A 198 MET cc_start: 0.8625 (mtt) cc_final: 0.8402 (tpp) REVERT: A 537 MET cc_start: 0.7455 (tpp) cc_final: 0.7244 (tpp) REVERT: A 539 MET cc_start: 0.9391 (ppp) cc_final: 0.9190 (ppp) REVERT: A 669 MET cc_start: 0.9419 (ppp) cc_final: 0.9198 (ppp) REVERT: A 718 MET cc_start: 0.8532 (ptt) cc_final: 0.7990 (ptt) REVERT: A 765 MET cc_start: 0.9571 (ppp) cc_final: 0.9289 (ppp) REVERT: A 766 MET cc_start: 0.9738 (mmp) cc_final: 0.9448 (mmm) REVERT: A 972 MET cc_start: 0.9139 (pmm) cc_final: 0.8599 (pmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3249 time to fit residues: 43.7369 Evaluate side-chains 75 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 234 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 292 GLN B 917 ASN ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20511 Z= 0.252 Angle : 0.593 9.156 27943 Z= 0.314 Chirality : 0.040 0.222 3081 Planarity : 0.004 0.050 3339 Dihedral : 16.530 149.277 3335 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2307 helix: 0.96 (0.17), residues: 959 sheet: -1.43 (0.31), residues: 306 loop : -1.46 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 931 HIS 0.006 0.001 HIS B 961 PHE 0.025 0.002 PHE B 417 TYR 0.018 0.002 TYR A 830 ARG 0.015 0.001 ARG A 982 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.6855 (ttt) cc_final: 0.6212 (tpt) REVERT: B 381 MET cc_start: 0.4424 (tpp) cc_final: 0.4168 (tpt) REVERT: B 669 MET cc_start: 0.9630 (ppp) cc_final: 0.9405 (ppp) REVERT: B 718 MET cc_start: 0.9613 (ptp) cc_final: 0.9339 (ptt) REVERT: B 765 MET cc_start: 0.9453 (mmp) cc_final: 0.9219 (mmp) REVERT: B 809 MET cc_start: 0.9273 (tpt) cc_final: 0.9038 (mmm) REVERT: B 847 MET cc_start: 0.9556 (mmp) cc_final: 0.9289 (tmm) REVERT: B 943 MET cc_start: 0.9648 (tpt) cc_final: 0.9309 (tpp) REVERT: B 972 MET cc_start: 0.9609 (mpp) cc_final: 0.9094 (mpp) REVERT: B 1131 MET cc_start: 0.9470 (mpp) cc_final: 0.9122 (mpp) REVERT: A 189 MET cc_start: 0.5517 (tpt) cc_final: 0.5190 (tpt) REVERT: A 198 MET cc_start: 0.8547 (mtt) cc_final: 0.8273 (tpp) REVERT: A 539 MET cc_start: 0.9464 (ppp) cc_final: 0.9207 (ppp) REVERT: A 669 MET cc_start: 0.9407 (ppp) cc_final: 0.9182 (ppp) REVERT: A 718 MET cc_start: 0.8683 (ptt) cc_final: 0.8151 (ptt) REVERT: A 765 MET cc_start: 0.9610 (ppp) cc_final: 0.9274 (ppp) REVERT: A 766 MET cc_start: 0.9765 (mmp) cc_final: 0.9517 (mmm) REVERT: A 972 MET cc_start: 0.9084 (pmm) cc_final: 0.8521 (pmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3105 time to fit residues: 42.1877 Evaluate side-chains 72 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 27 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 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 150 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS ** 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 445 ASN A 583 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.034762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.020070 restraints weight = 340875.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.020474 restraints weight = 223873.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.020985 restraints weight = 168069.286| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20511 Z= 0.228 Angle : 0.566 9.626 27943 Z= 0.300 Chirality : 0.039 0.190 3081 Planarity : 0.003 0.043 3339 Dihedral : 16.627 150.209 3335 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2307 helix: 0.95 (0.17), residues: 960 sheet: -1.47 (0.31), residues: 321 loop : -1.44 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 931 HIS 0.007 0.001 HIS B 961 PHE 0.017 0.002 PHE A 731 TYR 0.016 0.002 TYR A 892 ARG 0.007 0.001 ARG A 982 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.87 seconds wall clock time: 58 minutes 18.86 seconds (3498.86 seconds total)