Starting phenix.real_space_refine on Wed Mar 4 23:03:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi4_23839/03_2026/7mi4_23839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi4_23839/03_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_23839/03_2026/7mi4_23839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi4_23839/03_2026/7mi4_23839.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mi4_23839/03_2026/7mi4_23839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi4_23839/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.58, per 1000 atoms: 0.21 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: 1.52 Conformation dependent library (CDL) restraints added in 785.1 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: 1.97 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: 3.22 Time building geometry restraints manager: 2.07 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=" C PRO B 414 " pdb=" N PRO B 415 " ideal model delta sigma weight residual 1.335 1.310 0.025 8.70e-03 1.32e+04 8.57e+00 bond pdb=" C PRO D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 1.335 1.310 0.025 8.70e-03 1.32e+04 8.21e+00 bond pdb=" CA HIS D 301 " pdb=" C HIS D 301 " ideal model delta sigma weight residual 1.524 1.467 0.057 2.25e-02 1.98e+03 6.38e+00 bond pdb=" CA HIS B 301 " pdb=" C HIS B 301 " ideal model delta sigma weight residual 1.524 1.467 0.056 2.25e-02 1.98e+03 6.26e+00 bond pdb=" CB LYS F 22 " pdb=" CG LYS F 22 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.71e+00 ... (remaining 17687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 24062 3.77 - 7.54: 162 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: 1917 0.056 - 0.113: 590 0.113 - 0.169: 109 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.580 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.169 17700 Z= 0.411 Angle : 1.398 62.367 24286 Z= 0.557 Chirality : 0.054 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 covalent geometry : bond 0.00923 (17692) covalent geometry : angle 0.98440 (24262) hydrogen bonds : bond 0.12830 ( 818) hydrogen bonds : angle 6.09942 ( 2304) metal coordination : bond 0.09312 ( 8) metal coordination : angle 31.58736 ( 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 : 0.627 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: 0.1791 time to fit residues: 75.3776 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 : 0.372 ------------------------------------------------------------------------------- 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: 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 538 GLN B 361 GLN B 522 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN D 322 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105236 restraints weight = 27715.438| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.32 r_work: 0.3335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17700 Z= 0.144 Angle : 0.894 42.177 24286 Z= 0.351 Chirality : 0.043 0.146 2628 Planarity : 0.005 0.056 2928 Dihedral : 17.282 139.502 3047 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 1.94 % Allowed : 7.34 % Favored : 90.72 % 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: -0.72 (0.19), residues: 1966 helix: 1.08 (0.17), residues: 912 sheet: -1.21 (0.37), residues: 204 loop : -2.09 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 386 TYR 0.021 0.002 TYR C 527 PHE 0.024 0.001 PHE D 407 TRP 0.012 0.001 TRP E 17 HIS 0.007 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00315 (17692) covalent geometry : angle 0.64444 (24262) hydrogen bonds : bond 0.04231 ( 818) hydrogen bonds : angle 4.62256 ( 2304) metal coordination : bond 0.01263 ( 8) metal coordination : angle 19.70174 ( 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 256 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (t70) REVERT: A 363 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 516 MET cc_start: 0.9056 (mmm) cc_final: 0.8790 (mmt) REVERT: B 258 SER cc_start: 0.7400 (OUTLIER) cc_final: 0.6852 (m) REVERT: B 319 THR cc_start: 0.8335 (m) cc_final: 0.7883 (m) REVERT: B 323 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 343 TRP cc_start: 0.7550 (t-100) cc_final: 0.6692 (t60) REVERT: B 479 MET cc_start: 0.7517 (mmp) cc_final: 0.7151 (mmm) REVERT: B 483 ASN cc_start: 0.8389 (m-40) cc_final: 0.8055 (m-40) REVERT: C 280 GLU cc_start: 0.8786 (mp0) cc_final: 0.8536 (mp0) REVERT: C 326 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7699 (mmt-90) REVERT: C 465 MET cc_start: 0.8185 (ptm) cc_final: 0.7778 (ptm) REVERT: D 322 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7896 (t0) REVERT: D 342 ASN cc_start: 0.8331 (t0) cc_final: 0.7954 (m-40) REVERT: D 368 MET cc_start: 0.7922 (tmm) cc_final: 0.6522 (mtp) REVERT: E 24 MET cc_start: 0.9310 (mmm) cc_final: 0.9076 (mmp) REVERT: E 33 LEU cc_start: 0.8839 (tp) cc_final: 0.8510 (tp) REVERT: F 1 MET cc_start: 0.8152 (ttt) cc_final: 0.7925 (ttt) REVERT: F 8 SER cc_start: 0.8795 (p) cc_final: 0.8484 (p) outliers start: 32 outliers final: 10 residues processed: 242 average time/residue: 0.1522 time to fit residues: 52.9142 Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 116 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN B 420 ASN C 334 ASN C 420 ASN D 322 ASN D 420 ASN D 483 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN F 14 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088284 restraints weight = 27553.902| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.53 r_work: 0.2982 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17700 Z= 0.248 Angle : 0.775 30.676 24286 Z= 0.355 Chirality : 0.047 0.158 2628 Planarity : 0.005 0.047 2928 Dihedral : 17.144 141.600 3013 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 2.25 % Allowed : 10.01 % Favored : 87.74 % 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: -0.60 (0.19), residues: 1966 helix: 1.29 (0.17), residues: 898 sheet: -1.48 (0.34), residues: 236 loop : -2.02 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 432 TYR 0.016 0.002 TYR C 232 PHE 0.023 0.002 PHE D 525 TRP 0.013 0.002 TRP E 30 HIS 0.006 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00585 (17692) covalent geometry : angle 0.66157 (24262) hydrogen bonds : bond 0.04711 ( 818) hydrogen bonds : angle 4.59235 ( 2304) metal coordination : bond 0.02134 ( 8) metal coordination : angle 12.88241 ( 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 222 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.450 Fit side-chains REVERT: A 166 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8401 (t70) REVERT: A 363 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 485 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7378 (mt-10) REVERT: A 516 MET cc_start: 0.9072 (mmm) cc_final: 0.8816 (mmt) REVERT: A 526 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8686 (mmtp) REVERT: B 230 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8349 (mmtm) REVERT: B 258 SER cc_start: 0.7427 (OUTLIER) cc_final: 0.6867 (m) REVERT: B 323 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 417 ASP cc_start: 0.7172 (m-30) cc_final: 0.6699 (m-30) REVERT: D 259 GLN cc_start: 0.8310 (pt0) cc_final: 0.7970 (pt0) REVERT: D 322 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7975 (t0) REVERT: D 358 MET cc_start: 0.7623 (mmm) cc_final: 0.7412 (mmm) REVERT: E 77 LYS cc_start: 0.8662 (mttp) cc_final: 0.8371 (mttm) REVERT: F 8 SER cc_start: 0.8964 (p) cc_final: 0.8659 (p) REVERT: F 25 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.7930 (m-70) outliers start: 37 outliers final: 18 residues processed: 211 average time/residue: 0.1499 time to fit residues: 45.5817 Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 247 VAL Chi-restraints excluded: chain A residue 363 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 368 MET 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 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 25 HIS 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: chunk 104 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 194 optimal weight: 0.0010 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN D 342 ASN D 483 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 = 0.3609 r_free = 0.3609 target = 0.121278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091807 restraints weight = 27213.080| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.53 r_work: 0.3038 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17700 Z= 0.133 Angle : 0.649 20.236 24286 Z= 0.309 Chirality : 0.042 0.137 2628 Planarity : 0.004 0.043 2928 Dihedral : 17.034 140.245 3013 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 1.94 % Allowed : 10.50 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.25 (0.19), residues: 1966 helix: 1.70 (0.18), residues: 896 sheet: -1.32 (0.35), residues: 224 loop : -1.98 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 19 TYR 0.015 0.001 TYR D 527 PHE 0.022 0.001 PHE D 525 TRP 0.012 0.001 TRP E 17 HIS 0.003 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00299 (17692) covalent geometry : angle 0.57851 (24262) hydrogen bonds : bond 0.03801 ( 818) hydrogen bonds : angle 4.28006 ( 2304) metal coordination : bond 0.01213 ( 8) metal coordination : angle 9.37483 ( 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 225 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 358 MET cc_start: 0.8464 (tpp) cc_final: 0.8081 (tpt) REVERT: A 363 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8152 (t0) REVERT: A 485 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7341 (mt-10) REVERT: A 499 ASN cc_start: 0.8009 (m-40) cc_final: 0.7308 (m-40) REVERT: A 516 MET cc_start: 0.9067 (mmm) cc_final: 0.8785 (mmt) REVERT: A 526 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8710 (mmtp) REVERT: B 244 GLU cc_start: 0.7953 (tp30) cc_final: 0.7327 (mm-30) REVERT: B 323 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 479 MET cc_start: 0.7460 (mmm) cc_final: 0.6835 (mmm) REVERT: B 483 ASN cc_start: 0.8203 (m-40) cc_final: 0.7857 (m-40) REVERT: C 394 MET cc_start: 0.8808 (ptm) cc_final: 0.8577 (ptm) REVERT: C 465 MET cc_start: 0.7985 (ptm) cc_final: 0.7614 (ptm) REVERT: D 259 GLN cc_start: 0.8367 (pt0) cc_final: 0.8089 (pt0) REVERT: D 322 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7785 (t0) REVERT: D 368 MET cc_start: 0.7884 (tmm) cc_final: 0.6476 (mtm) REVERT: D 376 LEU cc_start: 0.8309 (tp) cc_final: 0.8029 (tp) REVERT: E 33 LEU cc_start: 0.8704 (tp) cc_final: 0.8292 (tp) REVERT: E 77 LYS cc_start: 0.8656 (mttp) cc_final: 0.8372 (mttm) REVERT: F 1 MET cc_start: 0.8170 (ttt) cc_final: 0.7901 (ttt) REVERT: F 8 SER cc_start: 0.8923 (p) cc_final: 0.8647 (p) REVERT: F 25 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.7608 (m-70) outliers start: 32 outliers final: 12 residues processed: 216 average time/residue: 0.1515 time to fit residues: 47.4098 Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 C residue 8 ILE 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 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain F residue 25 HIS 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: chunk 180 optimal weight: 0.8980 chunk 79 optimal weight: 0.0070 chunk 75 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 342 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 = 0.122125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092667 restraints weight = 27011.261| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.53 r_work: 0.3055 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17700 Z= 0.124 Angle : 0.622 18.028 24286 Z= 0.299 Chirality : 0.042 0.177 2628 Planarity : 0.004 0.040 2928 Dihedral : 17.013 138.878 3011 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 1.88 % Allowed : 11.65 % Favored : 86.47 % 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: -1.11 (0.37), residues: 206 loop : -1.99 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 19 TYR 0.015 0.001 TYR A 527 PHE 0.022 0.001 PHE D 525 TRP 0.010 0.001 TRP E 17 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00279 (17692) covalent geometry : angle 0.56273 (24262) hydrogen bonds : bond 0.03586 ( 818) hydrogen bonds : angle 4.14530 ( 2304) metal coordination : bond 0.01041 ( 8) metal coordination : angle 8.44717 ( 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 232 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.655 Fit side-chains REVERT: A 166 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8328 (t70) REVERT: A 351 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8528 (mmmt) REVERT: A 363 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 485 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7269 (mt-10) REVERT: A 499 ASN cc_start: 0.8000 (m-40) cc_final: 0.7273 (m-40) REVERT: A 516 MET cc_start: 0.9035 (mmm) cc_final: 0.8774 (mmt) REVERT: A 526 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8688 (mmtp) REVERT: B 244 GLU cc_start: 0.7963 (tp30) cc_final: 0.7447 (mm-30) REVERT: B 253 ARG cc_start: 0.6290 (mpt180) cc_final: 0.5870 (mpt180) REVERT: B 479 MET cc_start: 0.7439 (mmm) cc_final: 0.6790 (mmm) REVERT: B 483 ASN cc_start: 0.8257 (m-40) cc_final: 0.7921 (m-40) REVERT: C 394 MET cc_start: 0.8785 (ptm) cc_final: 0.8518 (ptm) REVERT: C 465 MET cc_start: 0.7962 (ptm) cc_final: 0.7512 (ptm) REVERT: D 259 GLN cc_start: 0.8315 (pt0) cc_final: 0.8017 (pt0) REVERT: D 322 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7958 (t0) REVERT: D 344 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6927 (ttt180) REVERT: D 376 LEU cc_start: 0.8288 (tp) cc_final: 0.8015 (tp) REVERT: D 433 GLU cc_start: 0.8416 (tp30) cc_final: 0.7801 (tp30) REVERT: E 22 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8395 (tttp) REVERT: E 24 MET cc_start: 0.9356 (mmm) cc_final: 0.9030 (mmp) REVERT: E 33 LEU cc_start: 0.8720 (tp) cc_final: 0.8293 (tp) REVERT: E 77 LYS cc_start: 0.8669 (mttp) cc_final: 0.8366 (mttt) REVERT: F 1 MET cc_start: 0.8120 (ttt) cc_final: 0.7850 (ttt) outliers start: 31 outliers final: 12 residues processed: 216 average time/residue: 0.1533 time to fit residues: 48.1312 Evaluate side-chains 205 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 247 VAL 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 506 LYS Chi-restraints excluded: chain C residue 8 ILE 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 322 ASN Chi-restraints excluded: chain D residue 441 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 342 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 = 0.3625 r_free = 0.3625 target = 0.122353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093003 restraints weight = 27161.690| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.54 r_work: 0.3059 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17700 Z= 0.121 Angle : 0.607 18.475 24286 Z= 0.293 Chirality : 0.041 0.150 2628 Planarity : 0.004 0.038 2928 Dihedral : 16.987 138.135 3009 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.56 % Rotamer: Outliers : 1.70 % Allowed : 12.68 % Favored : 85.62 % 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: 0.04 (0.20), residues: 1966 helix: 2.02 (0.18), residues: 886 sheet: -0.69 (0.40), residues: 184 loop : -2.00 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 15 TYR 0.014 0.001 TYR A 527 PHE 0.021 0.001 PHE D 525 TRP 0.009 0.001 TRP E 30 HIS 0.004 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00277 (17692) covalent geometry : angle 0.55423 (24262) hydrogen bonds : bond 0.03461 ( 818) hydrogen bonds : angle 4.07050 ( 2304) metal coordination : bond 0.00943 ( 8) metal coordination : angle 7.92729 ( 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 224 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.617 Fit side-chains REVERT: A 166 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8345 (t70) REVERT: A 351 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8467 (mmmt) REVERT: A 363 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8159 (t0) REVERT: A 485 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7328 (mt-10) REVERT: A 499 ASN cc_start: 0.8010 (m-40) cc_final: 0.7305 (m-40) REVERT: A 516 MET cc_start: 0.8998 (mmm) cc_final: 0.8708 (mmt) REVERT: A 526 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8715 (mmtp) REVERT: B 238 ASP cc_start: 0.8160 (t70) cc_final: 0.7918 (t0) REVERT: B 244 GLU cc_start: 0.7997 (tp30) cc_final: 0.7508 (mm-30) REVERT: B 253 ARG cc_start: 0.6169 (tpt170) cc_final: 0.5403 (mpt180) REVERT: B 416 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7058 (mmtp) REVERT: B 479 MET cc_start: 0.7352 (mmm) cc_final: 0.6711 (mmm) REVERT: B 483 ASN cc_start: 0.8256 (m-40) cc_final: 0.7929 (m-40) REVERT: B 506 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8582 (ttmm) REVERT: C 394 MET cc_start: 0.8697 (ptm) cc_final: 0.8421 (ptm) REVERT: C 465 MET cc_start: 0.7998 (ptm) cc_final: 0.7543 (ptm) REVERT: D 259 GLN cc_start: 0.8311 (pt0) cc_final: 0.7828 (pt0) REVERT: D 344 ARG cc_start: 0.7371 (mtp180) cc_final: 0.6917 (ttt180) REVERT: D 368 MET cc_start: 0.7966 (tmm) cc_final: 0.6609 (mtm) REVERT: D 376 LEU cc_start: 0.8293 (tp) cc_final: 0.8024 (tp) REVERT: D 433 GLU cc_start: 0.8456 (tp30) cc_final: 0.7916 (tp30) REVERT: E 22 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8448 (tttp) REVERT: E 24 MET cc_start: 0.9346 (mmm) cc_final: 0.9007 (mmp) REVERT: E 33 LEU cc_start: 0.8721 (tp) cc_final: 0.8283 (tp) REVERT: E 48 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8832 (ttm) REVERT: E 77 LYS cc_start: 0.8660 (mttp) cc_final: 0.8365 (mttt) REVERT: F 1 MET cc_start: 0.8156 (ttt) cc_final: 0.7880 (ttt) REVERT: F 25 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.7746 (m-70) outliers start: 28 outliers final: 13 residues processed: 211 average time/residue: 0.1538 time to fit residues: 46.7730 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 : 0.535 ------------------------------------------------------------------------------- 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 247 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG 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 193 VAL 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 265 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 GLU 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: chunk 189 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 179 optimal weight: 0.0870 chunk 185 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.091781 restraints weight = 27110.341| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.51 r_work: 0.3038 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17700 Z= 0.153 Angle : 0.626 19.480 24286 Z= 0.301 Chirality : 0.042 0.165 2628 Planarity : 0.004 0.040 2928 Dihedral : 17.044 138.177 3009 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 1.46 % Allowed : 13.59 % Favored : 84.95 % 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: 1.99 (0.18), residues: 886 sheet: -0.80 (0.39), residues: 196 loop : -1.99 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.017 0.001 TYR C 527 PHE 0.020 0.001 PHE D 525 TRP 0.009 0.001 TRP E 30 HIS 0.004 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00359 (17692) covalent geometry : angle 0.57633 (24262) hydrogen bonds : bond 0.03617 ( 818) hydrogen bonds : angle 4.09174 ( 2304) metal coordination : bond 0.01062 ( 8) metal coordination : angle 7.82758 ( 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 222 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8371 (t70) REVERT: A 351 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8380 (mmmt) REVERT: A 358 MET cc_start: 0.8404 (tpp) cc_final: 0.8097 (tpt) REVERT: A 363 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8135 (t0) REVERT: A 485 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7357 (mt-10) REVERT: A 499 ASN cc_start: 0.8020 (m-40) cc_final: 0.7282 (m-40) REVERT: A 516 MET cc_start: 0.8984 (mmm) cc_final: 0.8766 (mmt) REVERT: A 526 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8705 (mmtp) REVERT: B 238 ASP cc_start: 0.8107 (t70) cc_final: 0.7797 (t0) REVERT: B 244 GLU cc_start: 0.7975 (tp30) cc_final: 0.7457 (mm-30) REVERT: B 253 ARG cc_start: 0.6230 (tpt170) cc_final: 0.5589 (mpt180) REVERT: B 343 TRP cc_start: 0.7910 (t-100) cc_final: 0.7160 (t60) REVERT: B 416 LYS cc_start: 0.7528 (mtpt) cc_final: 0.7118 (mmtp) REVERT: C 318 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: C 394 MET cc_start: 0.8694 (ptm) cc_final: 0.8430 (ptm) REVERT: D 259 GLN cc_start: 0.8259 (pt0) cc_final: 0.7945 (pt0) REVERT: D 344 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7047 (ttt180) REVERT: D 376 LEU cc_start: 0.8316 (tp) cc_final: 0.8035 (tp) REVERT: D 433 GLU cc_start: 0.8498 (tp30) cc_final: 0.7970 (tp30) REVERT: E 22 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8495 (tttp) REVERT: E 77 LYS cc_start: 0.8694 (mttp) cc_final: 0.8406 (mttt) REVERT: F 1 MET cc_start: 0.8183 (ttt) cc_final: 0.7919 (ttt) REVERT: F 25 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7790 (m-70) outliers start: 24 outliers final: 12 residues processed: 210 average time/residue: 0.1537 time to fit residues: 46.1455 Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 247 VAL 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 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 193 VAL 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 265 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 29 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.0670 chunk 27 optimal weight: 0.0970 chunk 136 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 ASN 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 = 0.122886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093812 restraints weight = 27095.638| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.52 r_work: 0.3070 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17700 Z= 0.118 Angle : 0.607 18.840 24286 Z= 0.292 Chirality : 0.041 0.137 2628 Planarity : 0.004 0.037 2928 Dihedral : 17.007 137.473 3009 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 1.52 % Allowed : 13.96 % Favored : 84.53 % 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: 0.14 (0.20), residues: 1966 helix: 2.08 (0.18), residues: 886 sheet: -0.59 (0.40), residues: 184 loop : -1.93 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.014 0.001 TYR A 527 PHE 0.021 0.001 PHE D 525 TRP 0.010 0.001 TRP E 17 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00272 (17692) covalent geometry : angle 0.56120 (24262) hydrogen bonds : bond 0.03347 ( 818) hydrogen bonds : angle 3.99594 ( 2304) metal coordination : bond 0.00848 ( 8) metal coordination : angle 7.36845 ( 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 227 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6588 (pp20) REVERT: A 166 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8345 (t70) REVERT: A 358 MET cc_start: 0.8374 (tpp) cc_final: 0.8037 (tpt) REVERT: A 363 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 416 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.6963 (mmmt) REVERT: A 483 ASN cc_start: 0.8868 (m-40) cc_final: 0.8630 (m110) REVERT: A 485 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7295 (mt-10) REVERT: A 499 ASN cc_start: 0.8002 (m-40) cc_final: 0.7269 (m-40) REVERT: A 516 MET cc_start: 0.8978 (mmm) cc_final: 0.8751 (mmt) REVERT: B 238 ASP cc_start: 0.8052 (t70) cc_final: 0.7796 (t0) REVERT: B 244 GLU cc_start: 0.7944 (tp30) cc_final: 0.7431 (mm-30) REVERT: B 253 ARG cc_start: 0.6296 (tpt170) cc_final: 0.5595 (mpt180) REVERT: B 343 TRP cc_start: 0.7872 (t-100) cc_final: 0.7170 (t60) REVERT: B 416 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7176 (mmtp) REVERT: B 483 ASN cc_start: 0.8243 (m-40) cc_final: 0.7930 (m-40) REVERT: C 318 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: D 259 GLN cc_start: 0.8252 (pt0) cc_final: 0.7926 (pt0) REVERT: D 344 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7033 (ttt180) REVERT: D 376 LEU cc_start: 0.8267 (tp) cc_final: 0.7985 (tp) REVERT: D 403 MET cc_start: 0.4784 (mmm) cc_final: 0.4358 (mmp) REVERT: D 433 GLU cc_start: 0.8365 (tp30) cc_final: 0.7769 (tp30) REVERT: E 22 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8613 (ttpp) REVERT: E 33 LEU cc_start: 0.8740 (tp) cc_final: 0.8306 (tp) REVERT: E 77 LYS cc_start: 0.8693 (mttp) cc_final: 0.8420 (mttt) REVERT: F 1 MET cc_start: 0.8141 (ttt) cc_final: 0.7893 (ttt) REVERT: F 25 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.7705 (m-70) outliers start: 25 outliers final: 12 residues processed: 216 average time/residue: 0.1643 time to fit residues: 50.7412 Evaluate side-chains 212 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL 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 422 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 441 VAL Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 46 optimal weight: 0.0870 chunk 168 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093941 restraints weight = 27054.670| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.52 r_work: 0.3079 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17700 Z= 0.123 Angle : 0.611 18.683 24286 Z= 0.293 Chirality : 0.041 0.139 2628 Planarity : 0.004 0.037 2928 Dihedral : 16.990 137.112 3009 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.46 % Allowed : 13.96 % 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: 0.18 (0.20), residues: 1966 helix: 2.09 (0.18), residues: 888 sheet: -0.53 (0.40), residues: 184 loop : -1.90 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 49 TYR 0.014 0.001 TYR A 527 PHE 0.021 0.001 PHE D 525 TRP 0.009 0.001 TRP E 30 HIS 0.005 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00286 (17692) covalent geometry : angle 0.56642 (24262) hydrogen bonds : bond 0.03345 ( 818) hydrogen bonds : angle 3.97455 ( 2304) metal coordination : bond 0.00880 ( 8) metal coordination : angle 7.30263 ( 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 223 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6637 (pp20) REVERT: A 166 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8342 (t70) REVERT: A 236 ASP cc_start: 0.8410 (t0) cc_final: 0.7710 (t0) REVERT: A 363 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 416 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7078 (mmmt) REVERT: A 483 ASN cc_start: 0.8882 (m-40) cc_final: 0.8636 (m110) REVERT: A 485 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7305 (mt-10) REVERT: A 499 ASN cc_start: 0.7980 (m-40) cc_final: 0.7278 (m-40) REVERT: A 516 MET cc_start: 0.8988 (mmm) cc_final: 0.8757 (mmt) REVERT: B 238 ASP cc_start: 0.7996 (t70) cc_final: 0.7780 (t0) REVERT: B 244 GLU cc_start: 0.7950 (tp30) cc_final: 0.7432 (mm-30) REVERT: B 253 ARG cc_start: 0.6341 (tpt170) cc_final: 0.5582 (mpt180) REVERT: B 332 ILE cc_start: 0.8051 (tp) cc_final: 0.7582 (pt) REVERT: B 343 TRP cc_start: 0.7871 (t-100) cc_final: 0.7183 (t60) REVERT: B 416 LYS cc_start: 0.7546 (mtpt) cc_final: 0.7159 (mmtp) REVERT: C 236 ASP cc_start: 0.8149 (t0) cc_final: 0.7873 (t0) REVERT: C 318 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: D 259 GLN cc_start: 0.8239 (pt0) cc_final: 0.7923 (pt0) REVERT: D 376 LEU cc_start: 0.8304 (tp) cc_final: 0.8023 (tp) REVERT: D 403 MET cc_start: 0.4751 (mmm) cc_final: 0.4360 (mmp) REVERT: D 433 GLU cc_start: 0.8390 (tp30) cc_final: 0.7844 (tp30) REVERT: E 22 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8628 (ttpp) REVERT: E 33 LEU cc_start: 0.8718 (tp) cc_final: 0.8281 (tp) REVERT: E 77 LYS cc_start: 0.8699 (mttp) cc_final: 0.8414 (mttt) REVERT: F 1 MET cc_start: 0.8084 (ttt) cc_final: 0.7838 (ttt) REVERT: F 25 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.7731 (m-70) REVERT: F 57 ASN cc_start: 0.9081 (t0) cc_final: 0.8847 (t0) outliers start: 24 outliers final: 13 residues processed: 214 average time/residue: 0.1680 time to fit residues: 51.4720 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 : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL 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 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 25 HIS 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: chunk 163 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 156 optimal weight: 0.0870 chunk 200 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094075 restraints weight = 26969.980| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.55 r_work: 0.3085 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17700 Z= 0.116 Angle : 0.609 18.157 24286 Z= 0.293 Chirality : 0.041 0.147 2628 Planarity : 0.004 0.038 2928 Dihedral : 16.948 136.940 3009 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 1.21 % Allowed : 14.08 % Favored : 84.71 % 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: 0.25 (0.20), residues: 1966 helix: 2.16 (0.18), residues: 886 sheet: -0.44 (0.40), residues: 184 loop : -1.89 (0.20), residues: 896 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 0.023 0.001 PHE D 525 TRP 0.009 0.001 TRP E 17 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00268 (17692) covalent geometry : angle 0.56642 (24262) hydrogen bonds : bond 0.03270 ( 818) hydrogen bonds : angle 3.95368 ( 2304) metal coordination : bond 0.00815 ( 8) metal coordination : angle 7.09717 ( 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 219 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6602 (pp20) REVERT: A 166 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (t70) REVERT: A 363 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8111 (t0) REVERT: A 416 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7096 (mmmt) REVERT: A 485 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7268 (mt-10) REVERT: A 499 ASN cc_start: 0.7998 (m-40) cc_final: 0.7284 (m-40) REVERT: A 516 MET cc_start: 0.8970 (mmm) cc_final: 0.8742 (mmt) REVERT: B 238 ASP cc_start: 0.8058 (t70) cc_final: 0.7782 (t0) REVERT: B 244 GLU cc_start: 0.7972 (tp30) cc_final: 0.7445 (mm-30) REVERT: B 332 ILE cc_start: 0.8198 (tp) cc_final: 0.7770 (pt) REVERT: B 343 TRP cc_start: 0.7843 (t-100) cc_final: 0.7167 (t60) REVERT: B 416 LYS cc_start: 0.7535 (mtpt) cc_final: 0.7160 (mmtp) REVERT: C 236 ASP cc_start: 0.8234 (t0) cc_final: 0.7966 (t0) REVERT: D 259 GLN cc_start: 0.8248 (pt0) cc_final: 0.7937 (pt0) REVERT: D 376 LEU cc_start: 0.8290 (tp) cc_final: 0.8016 (tp) REVERT: D 433 GLU cc_start: 0.8397 (tp30) cc_final: 0.7897 (tp30) REVERT: E 22 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8645 (ttpp) REVERT: E 33 LEU cc_start: 0.8716 (tp) cc_final: 0.8289 (tp) REVERT: E 77 LYS cc_start: 0.8699 (mttp) cc_final: 0.8428 (mttt) REVERT: F 1 MET cc_start: 0.8132 (ttt) cc_final: 0.7886 (ttt) REVERT: F 25 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.7677 (m-70) REVERT: F 39 ARG cc_start: 0.8891 (ttt180) cc_final: 0.8686 (ttt180) outliers start: 20 outliers final: 12 residues processed: 212 average time/residue: 0.1562 time to fit residues: 47.7584 Evaluate side-chains 207 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 193 VAL 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 441 VAL Chi-restraints excluded: chain D residue 465 MET 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: chunk 143 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092774 restraints weight = 27204.101| |-----------------------------------------------------------------------------| r_work (start): 0.3185 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: 0.8141 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17700 Z= 0.144 Angle : 0.620 18.869 24286 Z= 0.299 Chirality : 0.042 0.159 2628 Planarity : 0.004 0.076 2928 Dihedral : 16.974 137.134 3009 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 1.27 % Allowed : 14.44 % Favored : 84.28 % 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: 0.22 (0.20), residues: 1966 helix: 2.13 (0.18), residues: 888 sheet: -0.41 (0.41), residues: 184 loop : -1.92 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.014 0.001 TYR A 527 PHE 0.023 0.001 PHE D 525 TRP 0.009 0.001 TRP E 30 HIS 0.005 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00340 (17692) covalent geometry : angle 0.57584 (24262) hydrogen bonds : bond 0.03456 ( 818) hydrogen bonds : angle 4.01179 ( 2304) metal coordination : bond 0.00960 ( 8) metal coordination : angle 7.35375 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.82 seconds wall clock time: 58 minutes 9.82 seconds (3489.82 seconds total)