Starting phenix.real_space_refine on Sun Oct 25 13:01:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi4_23839/10_2026/7mi4_23839.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 8 7.51 5 Fe 8 7.16 5 P 70 5.49 5 S 100 5.16 5 C 10594 2.51 5 N 3146 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17162 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4355 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 35, 'TRANS': 518} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4355 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 35, 'TRANS': 518} Chain: "D" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 717 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 717 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Unusual residues: {' MN': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 142 SG CYS A 22 72.626 59.201 118.374 1.00 50.21 S ATOM 1468 SG CYS A 196 67.121 60.303 119.003 1.00 54.73 S ATOM 1429 SG CYS A 190 67.978 56.403 114.756 1.00 55.03 S ATOM 1405 SG CYS A 187 70.056 61.435 114.328 1.00 56.92 S ATOM 7208 SG CYS C 22 50.242 66.716 54.499 1.00 52.30 S ATOM 8534 SG CYS C 196 55.355 64.535 53.489 1.00 53.19 S ATOM 8495 SG CYS C 190 52.700 61.667 57.813 1.00 55.11 S ATOM 8471 SG CYS C 187 53.864 66.976 58.343 1.00 57.72 S Time building chain proxies: 3.41, per 1000 atoms: 0.20 Number of scatterers: 17162 At special positions: 0 Unit cell: (115.62, 95.94, 174.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 Mn 8 24.99 S 100 16.00 P 70 15.00 O 3236 8.00 N 3146 7.00 C 10594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 714.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 187 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 190 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 196 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 22 " Number of angles added : 24 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 20 sheets defined 49.6% alpha, 14.3% beta 20 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.565A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.895A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 154 through 175 removed outlier: 3.816A pdb=" N GLY A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.681A pdb=" N ARG A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 316 through 342 Processing helix chain 'A' and resid 353 through 369 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.970A pdb=" N LEU A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.021A pdb=" N ARG A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 440 removed outlier: 4.066A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 467 through 483 removed outlier: 4.547A pdb=" N LEU A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.512A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.551A pdb=" N GLU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 300 through 315 removed outlier: 4.630A pdb=" N VAL B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.921A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 417 through 441 removed outlier: 3.536A pdb=" N VAL B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 removed outlier: 4.182A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Proline residue: B 467 - end of helix Proline residue: B 470 - end of helix Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 531 through 546 removed outlier: 4.196A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.565A pdb=" N VAL C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.895A pdb=" N ARG C 50 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 Processing helix chain 'C' and resid 154 through 175 removed outlier: 3.816A pdb=" N GLY C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.681A pdb=" N ARG C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 316 through 342 Processing helix chain 'C' and resid 353 through 369 Processing helix chain 'C' and resid 372 through 390 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.969A pdb=" N LEU C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 4.020A pdb=" N ARG C 410 " --> pdb=" O PHE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 440 removed outlier: 4.066A pdb=" N ARG C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 467 through 483 removed outlier: 4.547A pdb=" N LEU C 471 " --> pdb=" O PRO C 467 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 489 No H-bonds generated for 'chain 'C' and resid 487 through 489' Processing helix chain 'C' and resid 501 through 517 removed outlier: 3.512A pdb=" N ARG C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 547 removed outlier: 3.551A pdb=" N GLU C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 300 through 315 removed outlier: 4.630A pdb=" N VAL D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 343 Processing helix chain 'D' and resid 353 through 369 Processing helix chain 'D' and resid 372 through 390 removed outlier: 3.921A pdb=" N HIS D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'D' and resid 417 through 441 removed outlier: 3.537A pdb=" N VAL D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 removed outlier: 4.182A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Proline residue: D 467 - end of helix Proline residue: D 470 - end of helix Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 487 through 489 No H-bonds generated for 'chain 'D' and resid 487 through 489' Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 531 through 546 removed outlier: 4.197A pdb=" N GLU D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 28 Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'F' and resid 13 through 28 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.192A pdb=" N ILE A 11 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS A 85 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 83 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 76 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS A 85 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER A 74 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP A 87 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.192A pdb=" N ILE A 11 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS A 85 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE A 86 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR A 101 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR A 141 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP A 100 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 226 removed outlier: 7.192A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N THR A 284 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 260 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU A 286 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 262 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 284 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 222 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ALA B 261 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 224 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 251 removed outlier: 5.558A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS A 239 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 236 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 removed outlier: 6.855A pdb=" N ILE B 242 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 251 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 240 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.192A pdb=" N ILE C 11 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS C 85 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 83 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER C 76 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS C 85 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER C 74 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP C 87 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.192A pdb=" N ILE C 11 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS C 85 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE C 86 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR C 101 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR C 141 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP C 100 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 226 removed outlier: 7.191A pdb=" N LEU C 222 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA C 261 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 224 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 263 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 226 " --> pdb=" O PHE C 263 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N THR C 284 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 260 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU C 286 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 262 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 294 " --> pdb=" O TRP D 285 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR D 284 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 260 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 286 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU D 262 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU D 222 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ALA D 261 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 224 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 247 through 251 removed outlier: 5.558A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C 244 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS C 239 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP C 236 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AB6, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB7, first strand: chain 'D' and resid 248 through 251 removed outlier: 6.855A pdb=" N ILE D 242 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU D 251 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 240 " --> pdb=" O GLU D 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 491 through 493 Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 520 Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.502A pdb=" N VAL E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU E 4 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.764A pdb=" N LEU F 4 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 7677 1.42 - 1.64: 9841 1.64 - 1.85: 150 1.85 - 2.06: 0 2.06 - 2.28: 24 Bond restraints: 17692 Sorted by residual: bond pdb=" C3' DT G 5 " pdb=" O3' DT G 5 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" C3' DT H 5 " pdb=" O3' DT H 5 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.51e+01 bond pdb=" N1 DC G 15 " pdb=" C6 DC G 15 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.08e+01 bond pdb=" N1 DC H 14 " pdb=" C6 DC H 14 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.08e+01 bond pdb=" N1 DC G 14 " pdb=" C6 DC G 14 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 1.03e+01 ... (remaining 17687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 24060 3.77 - 7.54: 164 7.54 - 11.31: 26 11.31 - 15.07: 6 15.07 - 18.84: 6 Bond angle restraints: 24262 Sorted by residual: angle pdb=" CD ARG C 146 " pdb=" NE ARG C 146 " pdb=" CZ ARG C 146 " ideal model delta sigma weight residual 124.40 138.29 -13.89 1.40e+00 5.10e-01 9.85e+01 angle pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " ideal model delta sigma weight residual 124.40 138.29 -13.89 1.40e+00 5.10e-01 9.84e+01 angle pdb=" CG ARG B 386 " pdb=" CD ARG B 386 " pdb=" NE ARG B 386 " ideal model delta sigma weight residual 112.00 130.84 -18.84 2.20e+00 2.07e-01 7.34e+01 angle pdb=" CG ARG D 386 " pdb=" CD ARG D 386 " pdb=" NE ARG D 386 " ideal model delta sigma weight residual 112.00 130.83 -18.83 2.20e+00 2.07e-01 7.33e+01 angle pdb=" CA LYS E 22 " pdb=" CB LYS E 22 " pdb=" CG LYS E 22 " ideal model delta sigma weight residual 114.10 129.59 -15.49 2.00e+00 2.50e-01 6.00e+01 ... (remaining 24257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.45: 9600 28.45 - 56.91: 722 56.91 - 85.36: 100 85.36 - 113.81: 6 113.81 - 142.27: 2 Dihedral angle restraints: 10430 sinusoidal: 4762 harmonic: 5668 Sorted by residual: dihedral pdb=" CD ARG C 146 " pdb=" NE ARG C 146 " pdb=" CZ ARG C 146 " pdb=" NH1 ARG C 146 " ideal model delta sinusoidal sigma weight residual 0.00 -58.10 58.10 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " pdb=" NH1 ARG A 146 " ideal model delta sinusoidal sigma weight residual 0.00 -57.97 57.97 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CA ARG C 412 " pdb=" C ARG C 412 " pdb=" N ARG C 413 " pdb=" CA ARG C 413 " ideal model delta harmonic sigma weight residual 180.00 -147.75 -32.25 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 10427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1870 0.056 - 0.113: 614 0.113 - 0.169: 132 0.169 - 0.225: 10 0.225 - 0.282: 2 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA ARG C 146 " pdb=" N ARG C 146 " pdb=" C ARG C 146 " pdb=" CB ARG C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ARG A 146 " pdb=" N ARG A 146 " pdb=" C ARG A 146 " pdb=" CB ARG A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb="FE3 SF4 A 601 " pdb=" S1 SF4 A 601 " pdb=" S2 SF4 A 601 " pdb=" S4 SF4 A 601 " both_signs ideal model delta sigma weight residual False -10.55 -10.34 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2625 not shown) Planarity restraints: 2928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 146 " 0.412 9.50e-02 1.11e+02 1.97e-01 8.04e+01 pdb=" NE ARG C 146 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG C 146 " 0.128 2.00e-02 2.50e+03 pdb=" NH1 ARG C 146 " -0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG C 146 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 146 " -0.412 9.50e-02 1.11e+02 1.97e-01 8.01e+01 pdb=" NE ARG A 146 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 146 " -0.128 2.00e-02 2.50e+03 pdb=" NH1 ARG A 146 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 146 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 316 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 317 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " -0.036 5.00e-02 4.00e+02 ... (remaining 2925 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 32 2.25 - 2.91: 7345 2.91 - 3.58: 24815 3.58 - 4.24: 40707 4.24 - 4.90: 69391 Nonbonded interactions: 142290 Sorted by model distance: nonbonded pdb=" OP1 DG H 32 " pdb="MN MN H 801 " model vdw 1.590 2.320 nonbonded pdb=" NE2 HIS C 48 " pdb="MN MN C 603 " model vdw 1.827 2.400 nonbonded pdb=" NE2 HIS A 48 " pdb="MN MN H 801 " model vdw 1.828 2.400 nonbonded pdb=" OD2 ASP A 87 " pdb="MN MN H 801 " model vdw 1.848 2.320 nonbonded pdb=" OD2 ASP C 87 " pdb="MN MN C 603 " model vdw 1.848 2.320 ... (remaining 142285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 5 through 602) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 1 through 35) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.920 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.010 0.169 17700 Z= 0.511 Angle : 1.413 62.367 24286 Z= 0.615 Chirality : 0.056 0.282 2628 Planarity : 0.008 0.197 2928 Dihedral : 18.974 142.266 6802 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 5.83 % Allowed : 2.06 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1966 helix: 0.32 (0.17), residues: 922 sheet: -1.42 (0.34), residues: 236 loop : -2.12 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.133 0.002 ARG C 146 TYR 0.019 0.002 TYR D 545 PHE 0.023 0.002 PHE B 425 TRP 0.014 0.002 TRP F 30 HIS 0.011 0.002 HIS D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.51 (17692) covalent geometry : angle 1.00511 / 0.61 (24262) hydrogen bonds : bond 0.12830 / 9.28 ( 818) hydrogen bonds : angle 6.09942 / 4.42 ( 2304) metal coordination : bond 0.09312 / 4.38 ( 8) metal coordination : angle 31.58736 / 19.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 266 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7877 (m-30) cc_final: 0.7655 (m-30) REVERT: A 166 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 358 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (tpt) REVERT: A 479 MET cc_start: 0.7369 (mtp) cc_final: 0.7106 (mtt) REVERT: A 483 ASN cc_start: 0.8453 (m-40) cc_final: 0.8124 (m-40) REVERT: A 485 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7184 (mt-10) REVERT: A 516 MET cc_start: 0.8801 (mmm) cc_final: 0.8541 (mmm) REVERT: B 230 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7785 (mmtp) REVERT: B 258 SER cc_start: 0.7115 (OUTLIER) cc_final: 0.6615 (m) REVERT: B 302 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6488 (tpp80) REVERT: B 319 THR cc_start: 0.8086 (m) cc_final: 0.7617 (m) REVERT: B 323 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 343 TRP cc_start: 0.7177 (t-100) cc_final: 0.6729 (t-100) REVERT: B 479 MET cc_start: 0.7334 (mmp) cc_final: 0.7021 (mmm) REVERT: B 483 ASN cc_start: 0.8164 (m-40) cc_final: 0.7953 (m-40) REVERT: C 85 LYS cc_start: 0.8914 (tttt) cc_final: 0.8590 (ttmm) REVERT: C 162 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 417 ASP cc_start: 0.6889 (m-30) cc_final: 0.6455 (m-30) REVERT: D 259 GLN cc_start: 0.7982 (pt0) cc_final: 0.7562 (pt0) REVERT: D 293 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7563 (mmm) REVERT: D 342 ASN cc_start: 0.8119 (t0) cc_final: 0.7869 (m-40) REVERT: D 386 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7720 (ptm160) REVERT: D 429 MET cc_start: 0.8694 (mtm) cc_final: 0.8414 (mtm) REVERT: D 516 MET cc_start: 0.8454 (mmm) cc_final: 0.8029 (tpp) outliers start: 96 outliers final: 6 residues processed: 304 average time/residue: 0.1638 time to fit residues: 69.5659 Evaluate side-chains 195 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 386 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN B 361 GLN B 522 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092927 restraints weight = 26945.165| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.53 r_work: 0.3058 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17700 Z= 0.155 Angle : 1.010 48.727 24286 Z= 0.374 Chirality : 0.046 0.150 2628 Planarity : 0.005 0.047 2928 Dihedral : 17.400 138.514 3047 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.10 % Favored : 93.79 % Rotamer: Outliers : 1.76 % Allowed : 7.95 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1966 helix: 0.97 (0.17), residues: 902 sheet: -1.28 (0.39), residues: 180 loop : -2.11 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 19 TYR 0.020 0.002 TYR C 527 PHE 0.027 0.001 PHE D 407 TRP 0.013 0.001 TRP E 17 HIS 0.007 0.001 HIS D 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (17692) covalent geometry : angle 0.67663 / 0.37 (24262) hydrogen bonds : bond 0.04948 / 3.43 ( 818) hydrogen bonds : angle 4.81620 / 3.44 ( 2304) metal coordination : bond 0.01113 / 0.50 ( 8) metal coordination : angle 23.88049 / 15.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8207 (t0) REVERT: A 363 ASP cc_start: 0.8456 (m-30) cc_final: 0.8222 (t0) REVERT: A 409 THR cc_start: 0.8449 (p) cc_final: 0.8168 (p) REVERT: A 516 MET cc_start: 0.9047 (mmm) cc_final: 0.8791 (mmt) REVERT: B 258 SER cc_start: 0.7100 (OUTLIER) cc_final: 0.6440 (m) REVERT: B 319 THR cc_start: 0.8135 (m) cc_final: 0.7696 (m) REVERT: B 323 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 341 ARG cc_start: 0.7658 (mmp80) cc_final: 0.7148 (mmp80) REVERT: B 343 TRP cc_start: 0.7462 (t-100) cc_final: 0.6533 (t60) REVERT: B 479 MET cc_start: 0.7383 (mmp) cc_final: 0.7108 (mmm) REVERT: B 483 ASN cc_start: 0.8157 (m-40) cc_final: 0.7903 (m-40) REVERT: C 162 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8212 (mt) REVERT: C 280 GLU cc_start: 0.8573 (mp0) cc_final: 0.8367 (mp0) REVERT: C 326 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7286 (mmt-90) REVERT: C 417 ASP cc_start: 0.7006 (m-30) cc_final: 0.6444 (m-30) REVERT: C 465 MET cc_start: 0.8110 (ptm) cc_final: 0.7497 (ptm) REVERT: D 322 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7675 (t0) REVERT: D 342 ASN cc_start: 0.8127 (m-40) cc_final: 0.7694 (m-40) REVERT: D 360 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6483 (mp) REVERT: D 365 ARG cc_start: 0.8507 (ptm160) cc_final: 0.8292 (ptm-80) REVERT: D 368 MET cc_start: 0.7685 (tmm) cc_final: 0.6421 (mtp) REVERT: D 394 MET cc_start: 0.5036 (mtt) cc_final: 0.4647 (ttm) REVERT: D 518 GLN cc_start: 0.8294 (mt0) cc_final: 0.8084 (mt0) REVERT: E 33 LEU cc_start: 0.8669 (tp) cc_final: 0.8272 (tp) REVERT: F 8 SER cc_start: 0.8787 (p) cc_final: 0.8430 (p) REVERT: F 60 GLU cc_start: 0.8758 (pm20) cc_final: 0.8382 (pt0) outliers start: 29 outliers final: 9 residues processed: 228 average time/residue: 0.1467 time to fit residues: 49.0628 Evaluate side-chains 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 360 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [28, 54, 96, 116, 37, 120, 66, 179, 2, 7, 52] chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 ASN C 334 ASN C 420 ASN D 483 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.089477 restraints weight = 27596.292| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.51 r_work: 0.3010 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17700 Z= 0.227 Angle : 0.870 39.699 24286 Z= 0.363 Chirality : 0.047 0.155 2628 Planarity : 0.005 0.058 2928 Dihedral : 17.189 138.538 3015 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.31 % Favored : 93.59 % Rotamer: Outliers : 2.37 % Allowed : 9.65 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1966 helix: 1.15 (0.17), residues: 904 sheet: -1.51 (0.34), residues: 236 loop : -2.03 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 386 TYR 0.024 0.002 TYR C 527 PHE 0.021 0.002 PHE D 407 TRP 0.013 0.002 TRP E 30 HIS 0.005 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (17692) covalent geometry : angle 0.67036 / 0.36 (24262) hydrogen bonds : bond 0.04751 / 3.28 ( 818) hydrogen bonds : angle 4.67249 / 3.34 ( 2304) metal coordination : bond 0.01912 / 0.98 ( 8) metal coordination : angle 17.63933 / 11.59 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.594 Fit side-chains REVERT: A 166 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8378 (t70) REVERT: A 358 MET cc_start: 0.8490 (tpp) cc_final: 0.8066 (tpt) REVERT: A 363 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8159 (t0) REVERT: A 485 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7388 (mt-10) REVERT: A 516 MET cc_start: 0.9083 (mmm) cc_final: 0.8861 (mmm) REVERT: B 258 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.6868 (m) REVERT: B 323 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8125 (mp) REVERT: B 432 ARG cc_start: 0.8720 (ttt90) cc_final: 0.8330 (ttt90) REVERT: C 280 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: C 417 ASP cc_start: 0.7124 (m-30) cc_final: 0.6574 (m-30) REVERT: C 465 MET cc_start: 0.8147 (ptm) cc_final: 0.7771 (ptm) REVERT: D 259 GLN cc_start: 0.8382 (pt0) cc_final: 0.8082 (pt0) REVERT: D 342 ASN cc_start: 0.8115 (t0) cc_final: 0.7905 (t0) REVERT: D 358 MET cc_start: 0.7526 (mmm) cc_final: 0.7266 (mmm) REVERT: E 77 LYS cc_start: 0.8661 (mttp) cc_final: 0.8378 (mttm) REVERT: F 8 SER cc_start: 0.8966 (p) cc_final: 0.8617 (p) REVERT: F 22 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8459 (tptt) REVERT: F 25 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.7938 (m-70) outliers start: 39 outliers final: 17 residues processed: 219 average time/residue: 0.1423 time to fit residues: 45.2055 Evaluate side-chains 195 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [104, 59, 186, 194, 98, 79, 129, 199, 75, 113, 33] chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 186 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 483 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091584 restraints weight = 27488.485| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.46 r_work: 0.3043 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17700 Z= 0.152 Angle : 0.709 27.783 24286 Z= 0.327 Chirality : 0.044 0.190 2628 Planarity : 0.004 0.043 2928 Dihedral : 17.145 139.379 3013 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 2.37 % Allowed : 10.92 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1966 helix: 1.49 (0.18), residues: 908 sheet: -1.39 (0.37), residues: 196 loop : -2.01 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 44 TYR 0.017 0.001 TYR C 527 PHE 0.015 0.001 PHE D 407 TRP 0.013 0.001 TRP E 17 HIS 0.004 0.001 HIS D 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17692) covalent geometry : angle 0.60755 / 0.33 (24262) hydrogen bonds : bond 0.04124 / 2.81 ( 818) hydrogen bonds : angle 4.40611 / 3.14 ( 2304) metal coordination : bond 0.01394 / 0.71 ( 8) metal coordination : angle 11.64272 / 7.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.679 Fit side-chains REVERT: A 166 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8387 (t70) REVERT: A 363 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8152 (t0) REVERT: A 485 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7379 (mt-10) REVERT: A 516 MET cc_start: 0.9053 (mmm) cc_final: 0.8792 (mmt) REVERT: A 526 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8739 (mmtt) REVERT: A 536 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8390 (mt-10) REVERT: B 244 GLU cc_start: 0.7959 (tp30) cc_final: 0.7335 (mm-30) REVERT: B 258 SER cc_start: 0.7186 (OUTLIER) cc_final: 0.6754 (m) REVERT: B 323 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8080 (mp) REVERT: B 432 ARG cc_start: 0.8636 (ttt90) cc_final: 0.8226 (ttt90) REVERT: B 479 MET cc_start: 0.7296 (mmm) cc_final: 0.7009 (mmm) REVERT: C 47 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8555 (mmt-90) REVERT: C 236 ASP cc_start: 0.8217 (t0) cc_final: 0.8009 (t70) REVERT: C 293 MET cc_start: 0.9172 (tpp) cc_final: 0.8619 (mmt) REVERT: C 417 ASP cc_start: 0.7044 (m-30) cc_final: 0.6586 (m-30) REVERT: C 465 MET cc_start: 0.8012 (ptm) cc_final: 0.7671 (ptm) REVERT: D 259 GLN cc_start: 0.8403 (pt0) cc_final: 0.8051 (pt0) REVERT: D 342 ASN cc_start: 0.8204 (t0) cc_final: 0.7959 (t0) REVERT: D 358 MET cc_start: 0.7372 (mmm) cc_final: 0.7128 (mmm) REVERT: D 368 MET cc_start: 0.7901 (tmm) cc_final: 0.6465 (mtm) REVERT: D 376 LEU cc_start: 0.8350 (tp) cc_final: 0.8075 (tp) REVERT: D 518 GLN cc_start: 0.8258 (mt0) cc_final: 0.7920 (mt0) REVERT: E 32 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: E 33 LEU cc_start: 0.8760 (tp) cc_final: 0.8315 (tp) REVERT: E 77 LYS cc_start: 0.8641 (mttp) cc_final: 0.8376 (mttm) REVERT: F 8 SER cc_start: 0.8862 (p) cc_final: 0.8428 (p) REVERT: F 22 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8380 (tptt) outliers start: 39 outliers final: 20 residues processed: 225 average time/residue: 0.1523 time to fit residues: 49.4632 Evaluate side-chains 210 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [180, 79, 75, 139, 201, 98, 189, 74, 19, 130, 94] chunk 180 optimal weight: 0.7980 chunk 79 optimal weight: 0.0770 chunk 75 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 483 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.091865 restraints weight = 26797.647| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.53 r_work: 0.3044 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17700 Z= 0.128 Angle : 0.660 21.426 24286 Z= 0.313 Chirality : 0.043 0.138 2628 Planarity : 0.004 0.041 2928 Dihedral : 17.079 137.765 3013 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.76 % Allowed : 11.89 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1966 helix: 1.75 (0.18), residues: 896 sheet: -1.37 (0.35), residues: 226 loop : -1.94 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 19 TYR 0.015 0.001 TYR C 527 PHE 0.010 0.001 PHE C 40 TRP 0.010 0.001 TRP E 17 HIS 0.004 0.001 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17692) covalent geometry : angle 0.58573 / 0.31 (24262) hydrogen bonds : bond 0.03879 / 2.64 ( 818) hydrogen bonds : angle 4.27408 / 3.04 ( 2304) metal coordination : bond 0.01129 / 0.59 ( 8) metal coordination : angle 9.69910 / 6.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8325 (t70) REVERT: A 358 MET cc_start: 0.8429 (tpp) cc_final: 0.8041 (tpt) REVERT: A 363 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 374 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8426 (mp0) REVERT: A 485 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7369 (mt-10) REVERT: A 499 ASN cc_start: 0.8001 (m-40) cc_final: 0.7292 (m-40) REVERT: A 516 MET cc_start: 0.9049 (mmm) cc_final: 0.8762 (mmt) REVERT: B 244 GLU cc_start: 0.7944 (tp30) cc_final: 0.7438 (mm-30) REVERT: B 253 ARG cc_start: 0.6372 (mmt180) cc_final: 0.5869 (mmt-90) REVERT: B 323 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 432 ARG cc_start: 0.8585 (ttt90) cc_final: 0.8228 (ttt90) REVERT: B 479 MET cc_start: 0.7295 (mmm) cc_final: 0.6718 (mmm) REVERT: B 483 ASN cc_start: 0.8181 (m-40) cc_final: 0.7848 (m-40) REVERT: C 47 ARG cc_start: 0.8754 (mmp80) cc_final: 0.8543 (mmt-90) REVERT: C 236 ASP cc_start: 0.8243 (t0) cc_final: 0.7976 (t0) REVERT: C 394 MET cc_start: 0.8841 (ptm) cc_final: 0.8606 (ptm) REVERT: C 465 MET cc_start: 0.8071 (ptm) cc_final: 0.7491 (ptm) REVERT: D 259 GLN cc_start: 0.8346 (pt0) cc_final: 0.8081 (pt0) REVERT: D 376 LEU cc_start: 0.8296 (tp) cc_final: 0.8016 (tp) REVERT: D 433 GLU cc_start: 0.8419 (tp30) cc_final: 0.7810 (tp30) REVERT: D 518 GLN cc_start: 0.8238 (mt0) cc_final: 0.8020 (mt0) REVERT: E 24 MET cc_start: 0.9354 (mmm) cc_final: 0.9052 (mmp) REVERT: E 33 LEU cc_start: 0.8574 (tp) cc_final: 0.8113 (tp) REVERT: E 77 LYS cc_start: 0.8606 (mttp) cc_final: 0.8298 (mttt) REVERT: F 22 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8376 (tptt) REVERT: F 25 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7619 (m-70) outliers start: 29 outliers final: 17 residues processed: 217 average time/residue: 0.1491 time to fit residues: 47.1973 Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [56, 77, 17, 68, 1, 35, 71, 124, 186, 84, 21] chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 17 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 342 ASN D 483 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092948 restraints weight = 26965.153| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.3060 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17700 Z= 0.117 Angle : 0.633 17.708 24286 Z= 0.306 Chirality : 0.042 0.144 2628 Planarity : 0.004 0.039 2928 Dihedral : 17.033 137.433 3011 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 13.05 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 1966 helix: 1.93 (0.18), residues: 886 sheet: -1.08 (0.38), residues: 206 loop : -1.99 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 15 TYR 0.015 0.001 TYR C 527 PHE 0.011 0.001 PHE D 512 TRP 0.010 0.001 TRP F 17 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17692) covalent geometry : angle 0.57527 / 0.30 (24262) hydrogen bonds : bond 0.03661 / 2.49 ( 818) hydrogen bonds : angle 4.14462 / 2.95 ( 2304) metal coordination : bond 0.00972 / 0.50 ( 8) metal coordination : angle 8.45144 / 5.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.559 Fit side-chains REVERT: A 166 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8137 (t0) REVERT: A 351 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8554 (mmmt) REVERT: A 358 MET cc_start: 0.8406 (tpp) cc_final: 0.7960 (tpt) REVERT: A 363 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8128 (t0) REVERT: A 485 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7370 (mt-10) REVERT: A 499 ASN cc_start: 0.7991 (m-40) cc_final: 0.7270 (m-40) REVERT: A 516 MET cc_start: 0.9021 (mmm) cc_final: 0.8768 (mmt) REVERT: A 526 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8658 (mmtt) REVERT: B 244 GLU cc_start: 0.7928 (tp30) cc_final: 0.7443 (mm-30) REVERT: B 432 ARG cc_start: 0.8561 (ttt90) cc_final: 0.8194 (ttt90) REVERT: B 479 MET cc_start: 0.7332 (mmm) cc_final: 0.6772 (mmm) REVERT: B 483 ASN cc_start: 0.8232 (m-40) cc_final: 0.7901 (m-40) REVERT: B 506 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: C 72 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8697 (t) REVERT: C 236 ASP cc_start: 0.8168 (t0) cc_final: 0.7856 (t0) REVERT: C 293 MET cc_start: 0.9068 (tpp) cc_final: 0.8630 (mmt) REVERT: C 394 MET cc_start: 0.8793 (ptm) cc_final: 0.8528 (ptm) REVERT: C 465 MET cc_start: 0.8018 (ptm) cc_final: 0.7357 (ptm) REVERT: D 259 GLN cc_start: 0.8296 (pt0) cc_final: 0.7802 (pt0) REVERT: D 344 ARG cc_start: 0.7411 (mtp180) cc_final: 0.6963 (ttt180) REVERT: D 368 MET cc_start: 0.7963 (tmm) cc_final: 0.6542 (mtm) REVERT: D 376 LEU cc_start: 0.8264 (tp) cc_final: 0.7984 (tp) REVERT: D 433 GLU cc_start: 0.8407 (tp30) cc_final: 0.7748 (tp30) REVERT: D 518 GLN cc_start: 0.8344 (mt0) cc_final: 0.8141 (mt0) REVERT: E 24 MET cc_start: 0.9333 (mmm) cc_final: 0.8555 (mmp) REVERT: E 33 LEU cc_start: 0.8680 (tp) cc_final: 0.8233 (tp) REVERT: E 48 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8762 (ttm) REVERT: E 77 LYS cc_start: 0.8605 (mttp) cc_final: 0.8304 (mttt) REVERT: F 1 MET cc_start: 0.8110 (ttt) cc_final: 0.7853 (ttt) REVERT: F 22 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8336 (mmtp) REVERT: F 25 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7748 (m-70) outliers start: 27 outliers final: 12 residues processed: 212 average time/residue: 0.1435 time to fit residues: 43.8478 Evaluate side-chains 204 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [189, 8, 121, 51, 117, 179, 185, 17, 144, 49, 111] chunk 189 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092719 restraints weight = 26902.815| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.55 r_work: 0.3058 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17700 Z= 0.123 Angle : 0.629 18.678 24286 Z= 0.303 Chirality : 0.042 0.192 2628 Planarity : 0.004 0.039 2928 Dihedral : 17.018 137.045 3009 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.82 % Allowed : 12.92 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1966 helix: 1.97 (0.18), residues: 886 sheet: -1.01 (0.38), residues: 206 loop : -1.96 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 19 TYR 0.014 0.001 TYR A 527 PHE 0.032 0.001 PHE D 407 TRP 0.010 0.001 TRP F 17 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17692) covalent geometry : angle 0.57575 / 0.30 (24262) hydrogen bonds : bond 0.03665 / 2.50 ( 818) hydrogen bonds : angle 4.11729 / 2.93 ( 2304) metal coordination : bond 0.00964 / 0.50 ( 8) metal coordination : angle 8.05568 / 4.59 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.598 Fit side-chains REVERT: A 51 VAL cc_start: 0.7874 (m) cc_final: 0.7664 (m) REVERT: A 166 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8180 (t0) REVERT: A 351 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8507 (mmmt) REVERT: A 363 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 485 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7276 (mt-10) REVERT: A 499 ASN cc_start: 0.7996 (m-40) cc_final: 0.7269 (m-40) REVERT: A 516 MET cc_start: 0.9001 (mmm) cc_final: 0.8740 (mmt) REVERT: A 526 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8639 (mmtt) REVERT: B 244 GLU cc_start: 0.7960 (tp30) cc_final: 0.7435 (mm-30) REVERT: B 253 ARG cc_start: 0.6194 (mpt180) cc_final: 0.5916 (mpt180) REVERT: B 416 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7222 (mmtp) REVERT: B 432 ARG cc_start: 0.8567 (ttt90) cc_final: 0.8364 (tpt-90) REVERT: B 479 MET cc_start: 0.7315 (mmm) cc_final: 0.6762 (mmm) REVERT: B 483 ASN cc_start: 0.8231 (m-40) cc_final: 0.7896 (m-40) REVERT: B 506 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8479 (ttmm) REVERT: C 72 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8683 (t) REVERT: C 236 ASP cc_start: 0.8229 (t0) cc_final: 0.7900 (t0) REVERT: C 465 MET cc_start: 0.8002 (ptm) cc_final: 0.7354 (ptm) REVERT: D 259 GLN cc_start: 0.8333 (pt0) cc_final: 0.8035 (pt0) REVERT: D 344 ARG cc_start: 0.7436 (mtp180) cc_final: 0.6969 (ttt180) REVERT: D 376 LEU cc_start: 0.8263 (tp) cc_final: 0.7973 (tp) REVERT: D 433 GLU cc_start: 0.8412 (tp30) cc_final: 0.7792 (tp30) REVERT: E 33 LEU cc_start: 0.8698 (tp) cc_final: 0.8236 (tp) REVERT: E 77 LYS cc_start: 0.8620 (mttp) cc_final: 0.8313 (mttt) REVERT: F 1 MET cc_start: 0.8117 (ttt) cc_final: 0.7857 (ttt) REVERT: F 8 SER cc_start: 0.8860 (p) cc_final: 0.8627 (p) REVERT: F 25 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7813 (m-70) outliers start: 30 outliers final: 13 residues processed: 214 average time/residue: 0.1417 time to fit residues: 44.5649 Evaluate side-chains 207 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [29, 78, 88, 67, 21, 106, 27, 136, 74, 99, 6] chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 ASN D 342 ASN D 420 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090277 restraints weight = 26971.492| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.46 r_work: 0.3016 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17700 Z= 0.187 Angle : 0.668 20.484 24286 Z= 0.323 Chirality : 0.044 0.206 2628 Planarity : 0.005 0.042 2928 Dihedral : 17.146 137.522 3009 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.10 % Favored : 93.79 % Rotamer: Outliers : 1.52 % Allowed : 13.71 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1966 helix: 1.86 (0.18), residues: 886 sheet: -0.82 (0.39), residues: 196 loop : -2.01 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 15 TYR 0.015 0.001 TYR C 527 PHE 0.014 0.001 PHE D 425 TRP 0.010 0.001 TRP E 30 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (17692) covalent geometry : angle 0.61559 / 0.32 (24262) hydrogen bonds : bond 0.04065 / 2.79 ( 818) hydrogen bonds : angle 4.21649 / 3.01 ( 2304) metal coordination : bond 0.01324 / 0.70 ( 8) metal coordination : angle 8.24811 / 4.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.623 Fit side-chains REVERT: A 51 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7620 (m) REVERT: A 166 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8371 (t70) REVERT: A 351 LYS cc_start: 0.8828 (mttt) cc_final: 0.8441 (mmmt) REVERT: A 363 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 485 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7383 (mt-10) REVERT: A 516 MET cc_start: 0.8986 (mmm) cc_final: 0.8740 (mmt) REVERT: A 526 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8618 (mmtt) REVERT: B 244 GLU cc_start: 0.7905 (tp30) cc_final: 0.7407 (mm-30) REVERT: B 253 ARG cc_start: 0.6009 (mpt180) cc_final: 0.5742 (mpt180) REVERT: B 416 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7313 (mmtp) REVERT: B 432 ARG cc_start: 0.8649 (ttt90) cc_final: 0.8400 (tpt-90) REVERT: B 506 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8552 (ttmm) REVERT: B 518 GLN cc_start: 0.7728 (mt0) cc_final: 0.7511 (mt0) REVERT: C 72 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8708 (t) REVERT: C 236 ASP cc_start: 0.8364 (t0) cc_final: 0.8080 (t70) REVERT: C 417 ASP cc_start: 0.7071 (m-30) cc_final: 0.6633 (m-30) REVERT: D 259 GLN cc_start: 0.8317 (pt0) cc_final: 0.7994 (pt0) REVERT: D 376 LEU cc_start: 0.8307 (tp) cc_final: 0.8013 (tp) REVERT: D 433 GLU cc_start: 0.8463 (tp30) cc_final: 0.7869 (tp30) REVERT: D 518 GLN cc_start: 0.8357 (mt0) cc_final: 0.8072 (mt0) REVERT: E 22 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8524 (tttp) REVERT: E 77 LYS cc_start: 0.8666 (mttp) cc_final: 0.8367 (mttt) REVERT: F 8 SER cc_start: 0.8893 (p) cc_final: 0.8660 (p) REVERT: F 25 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.7609 (m-70) outliers start: 25 outliers final: 14 residues processed: 202 average time/residue: 0.1483 time to fit residues: 43.4877 Evaluate side-chains 205 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [73, 15, 45, 76, 142, 66, 154, 35, 182, 46, 168] chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092338 restraints weight = 27232.686| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.49 r_work: 0.3061 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17700 Z= 0.122 Angle : 0.643 19.715 24286 Z= 0.309 Chirality : 0.042 0.161 2628 Planarity : 0.004 0.039 2928 Dihedral : 17.063 137.641 3009 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 1.33 % Allowed : 14.08 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1966 helix: 1.98 (0.18), residues: 888 sheet: -0.67 (0.40), residues: 184 loop : -1.98 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 15 TYR 0.018 0.001 TYR C 527 PHE 0.011 0.001 PHE D 407 TRP 0.011 0.001 TRP E 17 HIS 0.004 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17692) covalent geometry : angle 0.59556 / 0.31 (24262) hydrogen bonds : bond 0.03690 / 2.52 ( 818) hydrogen bonds : angle 4.08835 / 2.92 ( 2304) metal coordination : bond 0.00891 / 0.46 ( 8) metal coordination : angle 7.75386 / 4.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.485 Fit side-chains REVERT: A 166 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8392 (t70) REVERT: A 358 MET cc_start: 0.8371 (tpp) cc_final: 0.8080 (tpt) REVERT: A 363 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 483 ASN cc_start: 0.8826 (m-40) cc_final: 0.8624 (m110) REVERT: A 485 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7300 (mt-10) REVERT: A 516 MET cc_start: 0.8997 (mmm) cc_final: 0.8737 (mmt) REVERT: B 238 ASP cc_start: 0.8075 (t70) cc_final: 0.7818 (t0) REVERT: B 244 GLU cc_start: 0.7925 (tp30) cc_final: 0.7416 (mm-30) REVERT: B 253 ARG cc_start: 0.6209 (mpt180) cc_final: 0.5635 (mpt180) REVERT: B 416 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7163 (mmtp) REVERT: B 432 ARG cc_start: 0.8603 (ttt90) cc_final: 0.8249 (tpt-90) REVERT: B 518 GLN cc_start: 0.7695 (mt0) cc_final: 0.7493 (mt0) REVERT: C 72 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (t) REVERT: C 236 ASP cc_start: 0.8351 (t0) cc_final: 0.8070 (t70) REVERT: C 293 MET cc_start: 0.9075 (tpp) cc_final: 0.8865 (mmt) REVERT: C 318 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: C 417 ASP cc_start: 0.7011 (m-30) cc_final: 0.6590 (m-30) REVERT: C 465 MET cc_start: 0.8017 (ptm) cc_final: 0.7505 (ptm) REVERT: D 259 GLN cc_start: 0.8322 (pt0) cc_final: 0.8000 (pt0) REVERT: D 376 LEU cc_start: 0.8267 (tp) cc_final: 0.7982 (tp) REVERT: D 433 GLU cc_start: 0.8389 (tp30) cc_final: 0.7865 (tp30) REVERT: E 22 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8541 (tttp) REVERT: E 33 LEU cc_start: 0.8738 (tp) cc_final: 0.8257 (tp) REVERT: E 77 LYS cc_start: 0.8683 (mttp) cc_final: 0.8394 (mttt) REVERT: F 8 SER cc_start: 0.8847 (p) cc_final: 0.8616 (p) REVERT: F 25 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7637 (m-70) REVERT: F 57 ASN cc_start: 0.9081 (t0) cc_final: 0.8790 (t0) outliers start: 22 outliers final: 10 residues processed: 207 average time/residue: 0.1482 time to fit residues: 44.8858 Evaluate side-chains 207 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [163, 65, 20, 112, 87, 97, 107, 118, 156, 200, 63] chunk 163 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 156 optimal weight: 0.0170 chunk 200 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093388 restraints weight = 27158.154| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.49 r_work: 0.3075 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17700 Z= 0.116 Angle : 0.636 19.262 24286 Z= 0.305 Chirality : 0.042 0.164 2628 Planarity : 0.004 0.038 2928 Dihedral : 16.998 136.557 3009 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 1.15 % Allowed : 14.26 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1966 helix: 2.03 (0.18), residues: 888 sheet: -0.59 (0.40), residues: 184 loop : -1.95 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 15 TYR 0.017 0.001 TYR C 527 PHE 0.016 0.001 PHE C 407 TRP 0.010 0.001 TRP E 17 HIS 0.004 0.001 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (17692) covalent geometry : angle 0.59070 / 0.30 (24262) hydrogen bonds : bond 0.03564 / 2.43 ( 818) hydrogen bonds : angle 4.06704 / 2.89 ( 2304) metal coordination : bond 0.00795 / 0.41 ( 8) metal coordination : angle 7.49826 / 3.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8370 (t70) REVERT: A 358 MET cc_start: 0.8284 (tpp) cc_final: 0.7968 (tpt) REVERT: A 363 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 416 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.6814 (mmmt) REVERT: A 483 ASN cc_start: 0.8832 (m-40) cc_final: 0.8610 (m110) REVERT: A 485 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7300 (mt-10) REVERT: A 499 ASN cc_start: 0.8017 (m-40) cc_final: 0.7278 (m-40) REVERT: A 516 MET cc_start: 0.8987 (mmm) cc_final: 0.8745 (mmt) REVERT: B 238 ASP cc_start: 0.8007 (t70) cc_final: 0.7758 (t0) REVERT: B 244 GLU cc_start: 0.7929 (tp30) cc_final: 0.7410 (mm-30) REVERT: B 343 TRP cc_start: 0.7902 (t-100) cc_final: 0.7188 (t60) REVERT: B 416 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7204 (mmtp) REVERT: B 432 ARG cc_start: 0.8584 (ttt90) cc_final: 0.8279 (ttt90) REVERT: C 72 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8583 (t) REVERT: C 236 ASP cc_start: 0.8372 (t0) cc_final: 0.8103 (t70) REVERT: C 293 MET cc_start: 0.9071 (tpp) cc_final: 0.8570 (mmt) REVERT: C 318 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: C 465 MET cc_start: 0.7992 (ptm) cc_final: 0.7540 (ptm) REVERT: D 259 GLN cc_start: 0.8276 (pt0) cc_final: 0.7981 (pt0) REVERT: D 376 LEU cc_start: 0.8277 (tp) cc_final: 0.8001 (tp) REVERT: D 433 GLU cc_start: 0.8456 (tp30) cc_final: 0.7898 (tp30) REVERT: E 22 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8542 (tttp) REVERT: E 33 LEU cc_start: 0.8725 (tp) cc_final: 0.8254 (tp) REVERT: E 77 LYS cc_start: 0.8688 (mttp) cc_final: 0.8415 (mttt) REVERT: F 8 SER cc_start: 0.8865 (p) cc_final: 0.8612 (p) REVERT: F 25 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.7749 (m-70) outliers start: 19 outliers final: 8 residues processed: 206 average time/residue: 0.1492 time to fit residues: 44.8985 Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [143, 170, 7, 83, 94, 115, 196, 167, 123, 24, 37] chunk 143 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092043 restraints weight = 27368.131| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.52 r_work: 0.3054 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17700 Z= 0.143 Angle : 0.651 19.650 24286 Z= 0.314 Chirality : 0.043 0.168 2628 Planarity : 0.004 0.038 2928 Dihedral : 17.026 136.771 3009 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.03 % Allowed : 14.32 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1966 helix: 2.00 (0.18), residues: 888 sheet: -0.61 (0.40), residues: 186 loop : -1.94 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 15 TYR 0.014 0.001 TYR A 527 PHE 0.012 0.001 PHE C 508 TRP 0.009 0.001 TRP F 17 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (17692) covalent geometry : angle 0.60667 / 0.31 (24262) hydrogen bonds : bond 0.03665 / 2.51 ( 818) hydrogen bonds : angle 4.10438 / 2.92 ( 2304) metal coordination : bond 0.01022 / 0.53 ( 8) metal coordination : angle 7.57486 / 3.98 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3267.85 seconds wall clock time: 56 minutes 47.01 seconds (3407.01 seconds total)