Starting phenix.real_space_refine on Tue Nov 19 13:00:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyx_28723/11_2024/8eyx_28723_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyx_28723/11_2024/8eyx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyx_28723/11_2024/8eyx_28723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyx_28723/11_2024/8eyx_28723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyx_28723/11_2024/8eyx_28723_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyx_28723/11_2024/8eyx_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-5513/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: 9.11, per 1000 atoms: 0.64 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=0, symmetry=0 Time building additional restraints: 4.04 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: 2.38 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: 6.21 Time building geometry restraints manager: 4.62 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: 1.86 - 2.47: 175 2.47 - 3.07: 10555 3.07 - 3.68: 24060 3.68 - 4.29: 34280 4.29 - 4.90: 53541 Nonbonded interactions: 122611 Sorted by model distance: nonbonded pdb=" CB PHE B 506 " pdb=" NE1 TRP B 529 " model vdw 1.857 3.520 nonbonded pdb=" CD2 PHE B 506 " pdb=" NE1 TRP B 529 " model vdw 1.876 3.420 nonbonded pdb=" CB PHE B 506 " pdb=" CD1 TRP B 529 " model vdw 1.932 3.660 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 ... (remaining 122606 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: 7.640 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: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.760 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- 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 : 0.006 0.267 14641 Z= 0.357 Angle : 0.758 12.422 19835 Z= 0.410 Chirality : 0.046 0.253 2150 Planarity : 0.005 0.086 2564 Dihedral : 12.875 101.852 5412 Min Nonbonded Distance : 1.857 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 *********************** 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 : 1.650 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: 0.3184 time to fit residues: 54.0118 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 : 1.779 ------------------------------------------------------------------------------- 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: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14641 Z= 0.186 Angle : 0.618 10.620 19835 Z= 0.324 Chirality : 0.045 0.179 2150 Planarity : 0.004 0.067 2564 Dihedral : 5.270 58.622 1935 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.33 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: -1.38 (0.20), residues: 1735 helix: -0.33 (0.33), residues: 240 sheet: -0.49 (0.28), residues: 352 loop : -1.22 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 529 HIS 0.010 0.001 HIS B 386 PHE 0.027 0.001 PHE A 264 TYR 0.020 0.001 TYR A 91 ARG 0.005 0.001 ARG A 796 *********************** 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 : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7509 (pmm) cc_final: 0.7211 (pmm) REVERT: A 36 LEU cc_start: 0.9378 (pt) cc_final: 0.8846 (pt) REVERT: A 404 ASP cc_start: 0.8693 (m-30) cc_final: 0.8476 (m-30) REVERT: A 833 MET cc_start: 0.8911 (tpt) cc_final: 0.8550 (tpt) REVERT: B 379 LEU cc_start: 0.9060 (tt) cc_final: 0.8392 (tt) REVERT: B 833 MET cc_start: 0.8975 (mmp) cc_final: 0.8219 (mmp) REVERT: E 69 TYR cc_start: 0.9094 (t80) cc_final: 0.8797 (t80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2701 time to fit residues: 37.7059 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 : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 158 optimal weight: 0.0270 chunk 171 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14641 Z= 0.164 Angle : 0.579 9.118 19835 Z= 0.299 Chirality : 0.044 0.200 2150 Planarity : 0.004 0.067 2564 Dihedral : 5.084 49.267 1935 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.80 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: -1.26 (0.21), residues: 1735 helix: 0.06 (0.33), residues: 231 sheet: -0.43 (0.29), residues: 348 loop : -1.20 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 634 HIS 0.007 0.001 HIS B 629 PHE 0.016 0.001 PHE F 24 TYR 0.026 0.001 TYR A 91 ARG 0.003 0.000 ARG A 114 *********************** 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 87 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7445 (pmm) cc_final: 0.7221 (pmm) REVERT: A 91 TYR cc_start: 0.8717 (m-10) cc_final: 0.8419 (m-10) REVERT: A 833 MET cc_start: 0.8901 (tpt) cc_final: 0.8504 (tpt) REVERT: B 358 LEU cc_start: 0.8514 (tt) cc_final: 0.8154 (mp) REVERT: B 379 LEU cc_start: 0.9031 (tt) cc_final: 0.8442 (tt) REVERT: B 535 ASP cc_start: 0.9141 (m-30) cc_final: 0.8836 (t0) REVERT: B 833 MET cc_start: 0.9009 (mmp) cc_final: 0.8431 (mmp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2871 time to fit residues: 38.7972 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 : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 20.0000 chunk 119 optimal weight: 0.0770 chunk 82 optimal weight: 50.0000 chunk 17 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 158 optimal weight: 40.0000 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 overall best weight: 1.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 199 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14641 Z= 0.201 Angle : 0.592 12.387 19835 Z= 0.304 Chirality : 0.044 0.218 2150 Planarity : 0.004 0.071 2564 Dihedral : 5.053 45.064 1935 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.86 % Favored : 92.85 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.82 % 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: -1.23 (0.21), residues: 1735 helix: 0.24 (0.34), residues: 230 sheet: -0.41 (0.28), residues: 362 loop : -1.22 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 529 HIS 0.010 0.001 HIS A 429 PHE 0.013 0.001 PHE B 382 TYR 0.022 0.001 TYR A 581 ARG 0.013 0.000 ARG B 252 *********************** 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 84 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7420 (pmm) cc_final: 0.7094 (pmm) REVERT: A 91 TYR cc_start: 0.8797 (m-10) cc_final: 0.8431 (m-10) REVERT: B 358 LEU cc_start: 0.8562 (tt) cc_final: 0.8132 (mp) REVERT: B 379 LEU cc_start: 0.9228 (tt) cc_final: 0.8976 (tt) REVERT: B 535 ASP cc_start: 0.9149 (m-30) cc_final: 0.8835 (t0) REVERT: B 833 MET cc_start: 0.9012 (mmp) cc_final: 0.8480 (mmp) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2384 time to fit residues: 32.6238 Evaluate side-chains 66 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14641 Z= 0.209 Angle : 0.586 9.908 19835 Z= 0.300 Chirality : 0.043 0.179 2150 Planarity : 0.004 0.070 2564 Dihedral : 5.081 41.565 1935 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.09 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -1.25 (0.21), residues: 1735 helix: 0.04 (0.33), residues: 242 sheet: -0.39 (0.28), residues: 362 loop : -1.21 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 553 HIS 0.008 0.001 HIS B 629 PHE 0.010 0.001 PHE B 382 TYR 0.019 0.001 TYR B 430 ARG 0.006 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 5 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 : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7474 (pmm) cc_final: 0.7107 (pmm) REVERT: A 91 TYR cc_start: 0.8837 (m-10) cc_final: 0.8464 (m-10) REVERT: A 137 LEU cc_start: 0.9290 (tp) cc_final: 0.9082 (tp) REVERT: B 358 LEU cc_start: 0.8538 (tt) cc_final: 0.8052 (mp) REVERT: B 379 LEU cc_start: 0.9247 (tt) cc_final: 0.8759 (tt) REVERT: B 535 ASP cc_start: 0.9160 (m-30) cc_final: 0.8858 (t0) REVERT: B 833 MET cc_start: 0.8984 (mmp) cc_final: 0.8494 (mmp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2518 time to fit residues: 33.3054 Evaluate side-chains 66 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 50.0000 chunk 162 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 275 HIS B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14641 Z= 0.185 Angle : 0.569 9.577 19835 Z= 0.291 Chirality : 0.043 0.168 2150 Planarity : 0.004 0.070 2564 Dihedral : 5.012 39.671 1935 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.74 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: -1.19 (0.21), residues: 1735 helix: 0.12 (0.33), residues: 242 sheet: -0.35 (0.28), residues: 362 loop : -1.18 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.006 0.001 HIS B 417 PHE 0.014 0.001 PHE B 382 TYR 0.017 0.001 TYR B 430 ARG 0.007 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 6 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 80 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7367 (pmm) cc_final: 0.7108 (pmm) REVERT: A 404 ASP cc_start: 0.8695 (m-30) cc_final: 0.8476 (m-30) REVERT: B 358 LEU cc_start: 0.8619 (tt) cc_final: 0.8212 (mp) REVERT: B 379 LEU cc_start: 0.9206 (tt) cc_final: 0.8617 (tt) REVERT: B 535 ASP cc_start: 0.9164 (m-30) cc_final: 0.8841 (t0) REVERT: B 833 MET cc_start: 0.8980 (mmp) cc_final: 0.8498 (mmp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1976 time to fit residues: 26.0971 Evaluate side-chains 66 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 108 ASN B 343 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14641 Z= 0.235 Angle : 0.605 14.030 19835 Z= 0.307 Chirality : 0.043 0.167 2150 Planarity : 0.004 0.069 2564 Dihedral : 5.091 37.279 1935 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.90 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -1.23 (0.21), residues: 1735 helix: 0.00 (0.33), residues: 252 sheet: -0.44 (0.28), residues: 368 loop : -1.18 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 493 HIS 0.009 0.001 HIS B 417 PHE 0.022 0.001 PHE A 477 TYR 0.024 0.001 TYR A 91 ARG 0.006 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 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 77 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7474 (pmm) cc_final: 0.7168 (pmm) REVERT: A 404 ASP cc_start: 0.8658 (m-30) cc_final: 0.8447 (m-30) REVERT: A 504 MET cc_start: 0.8146 (pmm) cc_final: 0.7943 (pmm) REVERT: A 833 MET cc_start: 0.8812 (tpt) cc_final: 0.8600 (tpt) REVERT: B 358 LEU cc_start: 0.8761 (tt) cc_final: 0.8449 (mp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2475 time to fit residues: 32.0807 Evaluate side-chains 62 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 146 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: