Starting phenix.real_space_refine on Tue May 20 03:35:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyx_28723/05_2025/8eyx_28723_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyx_28723/05_2025/8eyx_28723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyx_28723/05_2025/8eyx_28723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyx_28723/05_2025/8eyx_28723.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyx_28723/05_2025/8eyx_28723_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyx_28723/05_2025/8eyx_28723_neut.cif" } resolution = 4.5 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6287 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 9082 2.51 5 N 2447 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6572 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 769} Chain breaks: 4 Chain: "B" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6263 Classifications: {'peptide': 772} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 730} Chain breaks: 5 Chain: "D" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "F" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "G" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Time building chain proxies: 8.38, per 1000 atoms: 0.59 Number of scatterers: 14298 At special positions: 0 Unit cell: (145.8, 140.4, 176.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 2656 8.00 N 2447 7.00 C 9082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.02 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.02 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS G 62 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 66 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3334 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 34 sheets defined 17.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.542A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.525A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.703A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.994A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 378 through 382 removed outlier: 4.371A pdb=" N PHE A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.242A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.517A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.589A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.537A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.567A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.654A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.727A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.215A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 691 through 716 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.570A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.516A pdb=" N ASN E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.557A pdb=" N VAL F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 67 through 75 removed outlier: 3.774A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU F 72 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 3.540A pdb=" N VAL G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 67 through 75 removed outlier: 4.262A pdb=" N GLU G 72 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN G 73 " --> pdb=" O GLN G 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 5.802A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.329A pdb=" N HIS A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.680A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.680A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB3, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.258A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.743A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 504 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 601 through 609 removed outlier: 6.553A pdb=" N LYS A 616 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 605 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 614 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER A 607 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN A 612 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 764 Processing sheet with id=AB7, first strand: chain 'A' and resid 820 through 824 Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.122A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AC4, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC5, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC7, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.315A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 473 removed outlier: 6.127A pdb=" N GLU B 471 " --> pdb=" O LYS B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 477 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.636A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 567 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 609 removed outlier: 5.222A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 764 Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 Processing sheet with id=AD6, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD7, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.605A pdb=" N PHE B 905 " --> pdb=" O TYR B 884 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2382 1.32 - 1.44: 4034 1.44 - 1.57: 8086 1.57 - 1.69: 1 1.69 - 1.82: 138 Bond restraints: 14641 Sorted by residual: bond pdb=" CB TRP A 529 " pdb=" CG TRP A 529 " ideal model delta sigma weight residual 1.498 1.765 -0.267 3.10e-02 1.04e+03 7.40e+01 bond pdb=" CA TRP A 529 " pdb=" CB TRP A 529 " ideal model delta sigma weight residual 1.530 1.597 -0.066 1.69e-02 3.50e+03 1.55e+01 bond pdb=" N PRO B 548 " pdb=" CD PRO B 548 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.527 1.488 0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" CA TRP A 529 " pdb=" C TRP A 529 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.34e-02 5.57e+03 7.55e+00 ... (remaining 14636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19513 2.48 - 4.97: 284 4.97 - 7.45: 29 7.45 - 9.94: 5 9.94 - 12.42: 4 Bond angle restraints: 19835 Sorted by residual: angle pdb=" CA PRO B 548 " pdb=" N PRO B 548 " pdb=" CD PRO B 548 " ideal model delta sigma weight residual 112.00 99.58 12.42 1.40e+00 5.10e-01 7.87e+01 angle pdb=" N ALA A 466 " pdb=" CA ALA A 466 " pdb=" C ALA A 466 " ideal model delta sigma weight residual 108.99 119.30 -10.31 1.57e+00 4.06e-01 4.31e+01 angle pdb=" N PHE F 25 " pdb=" CA PHE F 25 " pdb=" C PHE F 25 " ideal model delta sigma weight residual 112.54 106.28 6.26 1.22e+00 6.72e-01 2.63e+01 angle pdb=" N CYS A 468 " pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 109.83 102.08 7.75 1.55e+00 4.16e-01 2.50e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 19830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.37: 8287 20.37 - 40.74: 487 40.74 - 61.11: 69 61.11 - 81.48: 21 81.48 - 101.85: 2 Dihedral angle restraints: 8866 sinusoidal: 3695 harmonic: 5171 Sorted by residual: dihedral pdb=" CA PRO B 272 " pdb=" C PRO B 272 " pdb=" N GLY B 273 " pdb=" CA GLY B 273 " ideal model delta harmonic sigma weight residual -180.00 -78.15 -101.85 0 5.00e+00 4.00e-02 4.15e+02 dihedral pdb=" CA THR A 580 " pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta harmonic sigma weight residual 180.00 147.84 32.16 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -138.17 52.17 1 1.00e+01 1.00e-02 3.71e+01 ... (remaining 8863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1673 0.051 - 0.101: 379 0.101 - 0.152: 81 0.152 - 0.202: 16 0.202 - 0.253: 1 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA TRP A 529 " pdb=" N TRP A 529 " pdb=" C TRP A 529 " pdb=" CB TRP A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 770 " pdb=" CB LEU A 770 " pdb=" CD1 LEU A 770 " pdb=" CD2 LEU A 770 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CG LEU B 358 " pdb=" CB LEU B 358 " pdb=" CD1 LEU B 358 " pdb=" CD2 LEU B 358 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 2147 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 547 " -0.062 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 548 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C THR A 580 " -0.053 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 271 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 272 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.043 5.00e-02 4.00e+02 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 186 2.48 - 3.09: 10866 3.09 - 3.69: 24089 3.69 - 4.30: 34183 4.30 - 4.90: 53282 Nonbonded interactions: 122606 Sorted by model distance: nonbonded pdb=" CD2 PHE B 506 " pdb=" NE1 TRP B 529 " model vdw 1.876 2.736 nonbonded pdb=" CG ARG B 267 " pdb=" NE2 GLN B 276 " model vdw 1.937 3.520 nonbonded pdb=" O GLN A 260 " pdb=" CD2 PHE A 264 " model vdw 1.960 3.340 nonbonded pdb=" OE1 GLN B 521 " pdb=" N ASN B 527 " model vdw 2.014 3.120 nonbonded pdb=" O THR B 516 " pdb=" CD2 PHE B 518 " model vdw 2.068 3.340 ... (remaining 122601 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' and (resid 5 through 151 or resid 208 through 540 or resid 548 throug \ h 908)) selection = (chain 'B' and (resid 5 through 521 or resid 527 through 540 or resid 548 throug \ h 658 or resid 705 through 908)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'F' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'G' and (resid 4 through 26 or resid 56 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.940 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.007 0.427 14682 Z= 0.447 Angle : 0.759 12.422 19915 Z= 0.410 Chirality : 0.046 0.253 2150 Planarity : 0.005 0.086 2564 Dihedral : 12.875 101.852 5412 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 33.88 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.74 % Favored : 89.68 % Rotamer: Outliers : 1.18 % Allowed : 1.24 % Favored : 97.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.73 (0.20), residues: 1735 helix: -0.98 (0.32), residues: 236 sheet: -0.65 (0.29), residues: 334 loop : -1.39 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 529 HIS 0.010 0.001 HIS B 629 PHE 0.016 0.002 PHE B 400 TYR 0.038 0.002 TYR A 512 ARG 0.005 0.001 ARG B 383 Details of bonding type rmsd hydrogen bonds : bond 0.19371 ( 361) hydrogen bonds : angle 8.31155 ( 942) SS BOND : bond 0.00379 ( 40) SS BOND : angle 0.95709 ( 80) covalent geometry : bond 0.00576 (14641) covalent geometry : angle 0.75813 (19835) Misc. bond : bond 0.42684 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7681 (pmm) cc_final: 0.7029 (pmm) REVERT: A 91 TYR cc_start: 0.8771 (m-10) cc_final: 0.8376 (m-10) REVERT: A 137 LEU cc_start: 0.9394 (tp) cc_final: 0.9148 (tp) REVERT: A 833 MET cc_start: 0.8869 (tpt) cc_final: 0.8488 (tpt) REVERT: B 379 LEU cc_start: 0.9097 (tt) cc_final: 0.8459 (tt) REVERT: B 833 MET cc_start: 0.9231 (mmp) cc_final: 0.8629 (mmp) REVERT: E 11 LEU cc_start: 0.9378 (tt) cc_final: 0.9163 (tp) REVERT: E 69 TYR cc_start: 0.9026 (t80) cc_final: 0.8758 (t80) outliers start: 19 outliers final: 5 residues processed: 115 average time/residue: 0.2905 time to fit residues: 49.4545 Evaluate side-chains 70 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 88 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 136 optimal weight: 0.0030 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 152 ASN A 777 HIS A 786 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 HIS B 790 GLN F 60 GLN G 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.049083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032464 restraints weight = 150766.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.033745 restraints weight = 91996.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.033434 restraints weight = 58129.835| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14682 Z= 0.134 Angle : 0.618 10.693 19915 Z= 0.324 Chirality : 0.045 0.178 2150 Planarity : 0.004 0.069 2564 Dihedral : 5.297 59.619 1935 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.92 % Favored : 92.74 % Rotamer: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.37 (0.20), residues: 1735 helix: -0.34 (0.33), residues: 240 sheet: -0.38 (0.28), residues: 348 loop : -1.25 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 529 HIS 0.009 0.001 HIS B 831 PHE 0.024 0.001 PHE A 264 TYR 0.020 0.001 TYR A 91 ARG 0.005 0.000 ARG A 796 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 361) hydrogen bonds : angle 7.09525 ( 942) SS BOND : bond 0.00321 ( 40) SS BOND : angle 0.87009 ( 80) covalent geometry : bond 0.00283 (14641) covalent geometry : angle 0.61711 (19835) Misc. bond : bond 0.00818 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7808 (pmm) cc_final: 0.7418 (pmm) REVERT: A 36 LEU cc_start: 0.9224 (pt) cc_final: 0.8596 (pt) REVERT: A 404 ASP cc_start: 0.8758 (m-30) cc_final: 0.8514 (m-30) REVERT: A 833 MET cc_start: 0.9064 (tpt) cc_final: 0.8750 (tpt) REVERT: B 300 MET cc_start: 0.9586 (mmm) cc_final: 0.9366 (mmm) REVERT: B 379 LEU cc_start: 0.9216 (tt) cc_final: 0.8797 (tt) REVERT: B 833 MET cc_start: 0.9054 (mmp) cc_final: 0.8465 (mmp) REVERT: E 69 TYR cc_start: 0.8898 (t80) cc_final: 0.8629 (t80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2641 time to fit residues: 36.6757 Evaluate side-chains 67 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.048046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.030229 restraints weight = 155526.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.031313 restraints weight = 86740.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.031962 restraints weight = 58640.346| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14682 Z= 0.181 Angle : 0.620 9.263 19915 Z= 0.320 Chirality : 0.044 0.188 2150 Planarity : 0.004 0.067 2564 Dihedral : 5.265 49.813 1935 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.72 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.21), residues: 1735 helix: 0.12 (0.34), residues: 227 sheet: -0.58 (0.28), residues: 357 loop : -1.23 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 529 HIS 0.010 0.001 HIS B 629 PHE 0.037 0.001 PHE B 506 TYR 0.027 0.001 TYR A 581 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 361) hydrogen bonds : angle 6.96598 ( 942) SS BOND : bond 0.00267 ( 40) SS BOND : angle 1.12268 ( 80) covalent geometry : bond 0.00394 (14641) covalent geometry : angle 0.61673 (19835) Misc. bond : bond 0.01426 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7786 (pmm) cc_final: 0.7337 (pmm) REVERT: A 91 TYR cc_start: 0.8743 (m-10) cc_final: 0.8497 (m-10) REVERT: A 404 ASP cc_start: 0.8686 (m-30) cc_final: 0.8468 (m-30) REVERT: B 379 LEU cc_start: 0.9236 (tt) cc_final: 0.8824 (tt) REVERT: B 833 MET cc_start: 0.9087 (mmp) cc_final: 0.8590 (mmp) REVERT: E 11 LEU cc_start: 0.9495 (tt) cc_final: 0.9206 (tp) REVERT: E 15 LEU cc_start: 0.9746 (mm) cc_final: 0.9516 (mm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2496 time to fit residues: 32.0774 Evaluate side-chains 64 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 152 optimal weight: 0.0050 chunk 87 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 108 ASN B 275 HIS B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.046987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.030927 restraints weight = 156029.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031080 restraints weight = 100414.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.031536 restraints weight = 72006.639| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14682 Z= 0.254 Angle : 0.687 11.872 19915 Z= 0.351 Chirality : 0.045 0.186 2150 Planarity : 0.004 0.069 2564 Dihedral : 5.457 45.080 1935 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.53 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.51 (0.20), residues: 1735 helix: -0.09 (0.33), residues: 237 sheet: -0.66 (0.27), residues: 371 loop : -1.37 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 529 HIS 0.011 0.001 HIS B 629 PHE 0.032 0.002 PHE B 506 TYR 0.025 0.002 TYR A 581 ARG 0.014 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 361) hydrogen bonds : angle 7.08608 ( 942) SS BOND : bond 0.00312 ( 40) SS BOND : angle 1.18783 ( 80) covalent geometry : bond 0.00539 (14641) covalent geometry : angle 0.68472 (19835) Misc. bond : bond 0.01339 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7911 (pmm) cc_final: 0.7353 (pmm) REVERT: A 91 TYR cc_start: 0.8966 (m-10) cc_final: 0.8629 (m-10) REVERT: A 404 ASP cc_start: 0.8759 (m-30) cc_final: 0.8554 (m-30) REVERT: B 300 MET cc_start: 0.9521 (mmp) cc_final: 0.9302 (mmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2340 time to fit residues: 27.5404 Evaluate side-chains 55 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.6242 > 50: distance: 121 - 231: 6.360 distance: 148 - 153: 34.098 distance: 154 - 155: 4.828 distance: 154 - 157: 25.106 distance: 155 - 156: 39.105 distance: 155 - 162: 36.869 distance: 157 - 158: 16.882 distance: 158 - 159: 20.628 distance: 159 - 160: 25.625 distance: 159 - 161: 33.654 distance: 162 - 163: 14.400 distance: 163 - 164: 38.533 distance: 163 - 166: 33.272 distance: 164 - 165: 37.460 distance: 164 - 173: 22.549 distance: 166 - 167: 45.385 distance: 167 - 168: 18.496 distance: 168 - 169: 5.251 distance: 169 - 170: 17.867 distance: 170 - 171: 4.172 distance: 170 - 172: 4.137 distance: 174 - 175: 35.806 distance: 174 - 177: 8.905 distance: 175 - 176: 7.949 distance: 175 - 179: 13.510 distance: 177 - 178: 26.017 distance: 179 - 180: 4.692 distance: 179 - 219: 24.254 distance: 180 - 181: 42.055 distance: 180 - 183: 33.143 distance: 181 - 182: 30.548 distance: 181 - 193: 34.467 distance: 183 - 184: 34.362 distance: 184 - 185: 13.478 distance: 184 - 186: 13.770 distance: 185 - 187: 12.593 distance: 186 - 188: 6.932 distance: 186 - 189: 8.755 distance: 187 - 188: 4.336 distance: 188 - 190: 11.088 distance: 189 - 191: 21.368 distance: 190 - 192: 12.037 distance: 191 - 192: 9.132 distance: 193 - 194: 4.833 distance: 194 - 195: 32.711 distance: 194 - 197: 28.209 distance: 195 - 196: 29.888 distance: 195 - 200: 40.673 distance: 197 - 198: 19.119 distance: 197 - 199: 19.405 distance: 200 - 201: 9.737 distance: 201 - 202: 49.471 distance: 201 - 204: 42.010 distance: 202 - 203: 9.672 distance: 202 - 210: 40.398 distance: 205 - 206: 23.873 distance: 205 - 207: 30.493 distance: 206 - 208: 24.766 distance: 207 - 209: 31.261 distance: 208 - 209: 20.800 distance: 210 - 211: 28.402 distance: 211 - 212: 17.075 distance: 211 - 214: 24.527 distance: 212 - 213: 54.193 distance: 212 - 216: 19.715 distance: 214 - 215: 18.258 distance: 216 - 217: 13.367 distance: 217 - 218: 33.855 distance: 217 - 220: 40.178 distance: 218 - 219: 12.956 distance: 218 - 226: 31.588 distance: 220 - 221: 26.171 distance: 221 - 222: 5.439 distance: 221 - 223: 19.777 distance: 222 - 224: 4.253 distance: 223 - 225: 13.301 distance: 224 - 225: 11.291 distance: 226 - 227: 13.041 distance: 227 - 228: 10.255 distance: 227 - 230: 23.208 distance: 228 - 229: 17.321 distance: 228 - 232: 24.660 distance: 230 - 231: 14.687 distance: 232 - 233: 7.667 distance: 233 - 234: 7.855 distance: 233 - 236: 6.819 distance: 234 - 235: 35.364 distance: 234 - 241: 4.004 distance: 236 - 237: 19.973 distance: 237 - 238: 9.091 distance: 238 - 239: 13.292 distance: 238 - 240: 10.088