Starting phenix.real_space_refine on Sun Jul 5 18:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vb0_31873/07_2026/7vb0_31873.map" } resolution = 3.6 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= 0.004 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29553 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.38, per 1000 atoms: 0.22 Number of scatterers: 29553 At special positions: 0 Unit cell: (149.85, 144.99, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 8.00 N 5131 7.00 C 18735 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 26 sheets defined 46.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.909A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.225A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 353 through 364 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.858A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.827A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 541 Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.000A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.714A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.540A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 315 removed outlier: 4.744A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.627A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.756A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.132A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.510A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.609A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.119A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.240A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.952A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.702A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.556A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.118A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.917A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 477 through 495 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.852A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 558 through 577 removed outlier: 3.532A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.665A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.089A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.554A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.559A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.856A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.594A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.534A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.830A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.631A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 359 through 365 removed outlier: 4.063A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.005A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.871A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 458 through 463 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.527A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 90' Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 212 through 215 removed outlier: 3.938A pdb=" N SER F 215 " --> pdb=" O GLY F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 229 through 250 removed outlier: 3.868A pdb=" N LEU F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.919A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.087A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.555A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.711A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.808A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.621A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.613A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 4.088A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 4.120A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 209 removed outlier: 5.254A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix removed outlier: 3.569A pdb=" N GLU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.738A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 40 Processing helix chain 'H' and resid 55 through 60 removed outlier: 4.038A pdb=" N GLU H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.749A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 119 removed outlier: 3.746A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 removed outlier: 4.318A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.581A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 131 Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.423A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.633A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 removed outlier: 3.893A pdb=" N ALA K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 93 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 127 through 139 removed outlier: 4.820A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.439A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.581A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.724A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 5.823A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.585A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.467A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 51 removed outlier: 5.708A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR E 54 " --> pdb=" O SER E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.599A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.512A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 148 removed outlier: 6.418A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.821A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 382 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.525A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.631A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB6, first strand: chain 'D' and resid 6 through 8 removed outlier: 6.267A pdb=" N THR J 161 " --> pdb=" O GLY J 156 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA J 120 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.509A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.605A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC2, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.251A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC5, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.234A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.503A pdb=" N THR F 172 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC8, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.767A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1285 hydrogen bonds defined for protein. 3702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 10097 1.37 - 1.51: 8742 1.51 - 1.66: 11075 1.66 - 1.80: 188 1.80 - 1.95: 8 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.581 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C8 ADP A 602 " pdb=" N7 ADP A 602 " ideal model delta sigma weight residual 1.350 1.310 0.040 2.00e-02 2.50e+03 4.01e+00 bond pdb=" C5 ADP A 602 " pdb=" N7 ADP A 602 " ideal model delta sigma weight residual 1.350 1.387 -0.037 2.00e-02 2.50e+03 3.45e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 40588 2.78 - 5.56: 199 5.56 - 8.35: 13 8.35 - 11.13: 6 11.13 - 13.91: 1 Bond angle restraints: 40807 Sorted by residual: angle pdb=" O2B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 105.99 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C ALA K 86 " pdb=" N ARG K 87 " pdb=" CA ARG K 87 " ideal model delta sigma weight residual 122.06 115.74 6.32 1.86e+00 2.89e-01 1.16e+01 angle pdb=" C ILE F 352 " pdb=" N ASP F 353 " pdb=" CA ASP F 353 " ideal model delta sigma weight residual 121.20 116.51 4.69 1.40e+00 5.10e-01 1.12e+01 angle pdb=" N ILE D 100 " pdb=" CA ILE D 100 " pdb=" C ILE D 100 " ideal model delta sigma weight residual 113.20 109.98 3.22 9.60e-01 1.09e+00 1.12e+01 angle pdb=" CA LEU L 148 " pdb=" CB LEU L 148 " pdb=" CG LEU L 148 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.83e+00 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.86: 17333 22.86 - 45.72: 865 45.72 - 68.59: 93 68.59 - 91.45: 41 91.45 - 114.31: 1 Dihedral angle restraints: 18333 sinusoidal: 7511 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 54.31 -114.31 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" CA ARG K 87 " pdb=" C ARG K 87 " pdb=" N TYR K 88 " pdb=" CA TYR K 88 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA LYS C 243 " pdb=" C LYS C 243 " pdb=" N TRP C 244 " pdb=" CA TRP C 244 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 18330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3106 0.036 - 0.073: 976 0.073 - 0.109: 399 0.109 - 0.145: 89 0.145 - 0.182: 6 Chirality restraints: 4576 Sorted by residual: chirality pdb=" CA ARG K 87 " pdb=" N ARG K 87 " pdb=" C ARG K 87 " pdb=" CB ARG K 87 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG K 89 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ARG K 89 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG K 89 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU K 90 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO F 324 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO E 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 246 2.57 - 3.15: 23706 3.15 - 3.73: 47846 3.73 - 4.32: 66089 4.32 - 4.90: 111004 Nonbonded interactions: 248891 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.982 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B AGS E 601 " model vdw 2.041 2.170 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.175 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.183 3.040 ... (remaining 248886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.630 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.520 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.003 0.106 30112 Z= 0.149 Angle : 0.550 13.911 40807 Z= 0.292 Chirality : 0.043 0.182 4576 Planarity : 0.004 0.045 5333 Dihedral : 13.487 114.308 11415 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.96 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1556 sheet: -0.45 (0.22), residues: 561 loop : 0.39 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 106 TYR 0.010 0.001 TYR D 463 PHE 0.026 0.001 PHE B 269 TRP 0.013 0.001 TRP F 471 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (30110) covalent geometry : angle 0.55008 / 0.29 (40807) hydrogen bonds : bond 0.13823 / 9.57 ( 1285) hydrogen bonds : angle 5.69567 / 3.95 ( 3702) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7794 (ttmm) REVERT: A 112 ASP cc_start: 0.7708 (t0) cc_final: 0.7475 (t70) REVERT: A 161 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6740 (mmmt) REVERT: A 197 ARG cc_start: 0.7808 (ptm-80) cc_final: 0.7137 (ptp90) REVERT: A 323 MET cc_start: 0.7771 (mpp) cc_final: 0.7130 (mmm) REVERT: A 342 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6326 (mm-30) REVERT: A 363 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6541 (tp30) REVERT: A 423 ASN cc_start: 0.8176 (t0) cc_final: 0.7909 (t0) REVERT: A 491 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6928 (mtm-85) REVERT: A 550 ARG cc_start: 0.7479 (mmt180) cc_final: 0.6910 (mmm-85) REVERT: B 29 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7590 (mttm) REVERT: B 130 ARG cc_start: 0.7065 (mpp-170) cc_final: 0.6775 (mtm110) REVERT: B 144 THR cc_start: 0.7954 (m) cc_final: 0.7589 (t) REVERT: B 236 VAL cc_start: 0.6915 (t) cc_final: 0.6639 (t) REVERT: B 282 MET cc_start: 0.8527 (mmm) cc_final: 0.8142 (mmt) REVERT: B 408 ARG cc_start: 0.6655 (ttm-80) cc_final: 0.6202 (tpp80) REVERT: B 417 ARG cc_start: 0.6622 (mmp-170) cc_final: 0.5538 (mmm-85) REVERT: B 424 TRP cc_start: 0.6597 (p90) cc_final: 0.6094 (p90) REVERT: B 458 LEU cc_start: 0.6393 (mm) cc_final: 0.6094 (mt) REVERT: B 459 GLN cc_start: 0.7343 (tp-100) cc_final: 0.6969 (mm-40) REVERT: B 477 GLN cc_start: 0.4030 (tp-100) cc_final: 0.3682 (mp10) REVERT: C 197 ARG cc_start: 0.6405 (ttp-110) cc_final: 0.6135 (ptm160) REVERT: C 332 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6614 (mt-10) REVERT: C 344 MET cc_start: 0.7259 (ttp) cc_final: 0.6652 (ttt) REVERT: C 393 GLU cc_start: 0.7053 (pp20) cc_final: 0.6569 (mm-30) REVERT: C 410 ASP cc_start: 0.7873 (t0) cc_final: 0.7500 (p0) REVERT: C 425 ASN cc_start: 0.8209 (t0) cc_final: 0.7905 (t0) REVERT: C 524 LYS cc_start: 0.6999 (ptmm) cc_final: 0.6640 (pttp) REVERT: C 550 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7314 (mtp85) REVERT: C 567 MET cc_start: 0.7288 (mmp) cc_final: 0.5990 (mtm) REVERT: D 7 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6378 (mp0) REVERT: D 52 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7134 (mt-10) REVERT: D 274 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7210 (mtt180) REVERT: D 275 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6992 (pt0) REVERT: D 353 ASP cc_start: 0.7324 (t0) cc_final: 0.7070 (t0) REVERT: D 363 ASN cc_start: 0.7461 (m-40) cc_final: 0.7082 (p0) REVERT: D 428 GLN cc_start: 0.7616 (mt0) cc_final: 0.7393 (tt0) REVERT: D 437 GLN cc_start: 0.6895 (tt0) cc_final: 0.6357 (tp40) REVERT: E 25 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7903 (ptpp) REVERT: E 81 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7485 (mtt90) REVERT: E 100 ILE cc_start: 0.8198 (pt) cc_final: 0.7616 (tt) REVERT: E 223 LYS cc_start: 0.6876 (mttt) cc_final: 0.6541 (ttmm) REVERT: E 318 ASP cc_start: 0.6876 (m-30) cc_final: 0.6629 (t0) REVERT: E 442 LEU cc_start: 0.6538 (mm) cc_final: 0.6304 (mt) REVERT: F 128 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6767 (pt0) REVERT: F 346 LYS cc_start: 0.7098 (mttt) cc_final: 0.6761 (mptt) REVERT: F 445 MET cc_start: 0.7560 (mtp) cc_final: 0.6934 (mtm) REVERT: G 19 ARG cc_start: 0.6257 (mtm-85) cc_final: 0.5687 (mtt-85) REVERT: G 71 ASP cc_start: 0.4183 (t0) cc_final: 0.3422 (m-30) REVERT: G 152 GLU cc_start: 0.6400 (tt0) cc_final: 0.5968 (tp30) REVERT: H 104 LEU cc_start: 0.3656 (mt) cc_final: 0.3429 (mm) REVERT: J 78 GLU cc_start: 0.3917 (tp30) cc_final: 0.3704 (tp30) REVERT: J 84 ARG cc_start: 0.3123 (mmt90) cc_final: 0.2624 (mmm160) REVERT: J 97 LYS cc_start: 0.6510 (mtpt) cc_final: 0.6263 (mptt) REVERT: J 102 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6822 (tm-30) REVERT: J 168 LEU cc_start: 0.5052 (tt) cc_final: 0.4726 (mt) REVERT: K 102 LYS cc_start: 0.4914 (tptp) cc_final: 0.4604 (pttt) REVERT: L 153 ARG cc_start: 0.5480 (ttm-80) cc_final: 0.4783 (tmm-80) REVERT: L 162 GLN cc_start: 0.6105 (pt0) cc_final: 0.5300 (mt0) outliers start: 0 outliers final: 0 residues processed: 599 average time/residue: 0.2359 time to fit residues: 211.6544 Evaluate side-chains 310 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 496 GLN B 246 ASN B 541 GLN C 109 HIS C 477 GLN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 364 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN ** L 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101484 restraints weight = 49599.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100643 restraints weight = 86687.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101425 restraints weight = 76903.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101897 restraints weight = 52999.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102072 restraints weight = 43885.624| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 30112 Z= 0.365 Angle : 0.797 12.405 40807 Z= 0.406 Chirality : 0.053 0.189 4576 Planarity : 0.007 0.101 5333 Dihedral : 5.904 80.323 4209 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.82 % Allowed : 10.22 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: -0.13 (0.14), residues: 3764 helix: 0.53 (0.13), residues: 1555 sheet: -0.94 (0.21), residues: 605 loop : -0.16 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 72 TYR 0.026 0.003 TYR F 13 PHE 0.031 0.003 PHE B 415 TRP 0.026 0.003 TRP B 119 HIS 0.009 0.002 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00873 / 0.37 (30110) covalent geometry : angle 0.79737 / 0.41 (40807) hydrogen bonds : bond 0.05465 / 3.68 ( 1285) hydrogen bonds : angle 5.12581 / 3.54 ( 3702) Misc. bond : bond 0.00570 / 0.28 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: A 246 ASN cc_start: 0.8388 (p0) cc_final: 0.8159 (p0) REVERT: A 323 MET cc_start: 0.7438 (mpp) cc_final: 0.7216 (mmm) REVERT: B 85 ASP cc_start: 0.7290 (p0) cc_final: 0.6859 (p0) REVERT: B 282 MET cc_start: 0.8176 (mmm) cc_final: 0.7970 (mmt) REVERT: B 408 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6715 (tpp80) REVERT: B 417 ARG cc_start: 0.6797 (mmp-170) cc_final: 0.5911 (mmm-85) REVERT: B 424 TRP cc_start: 0.7093 (p90) cc_final: 0.6797 (p90) REVERT: B 458 LEU cc_start: 0.7489 (mm) cc_final: 0.6945 (mt) REVERT: C 294 MET cc_start: 0.8305 (mtt) cc_final: 0.7937 (mtt) REVERT: C 550 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7273 (mtp85) REVERT: D 353 ASP cc_start: 0.7220 (t0) cc_final: 0.7003 (t0) REVERT: E 3 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6863 (pt) REVERT: E 57 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8730 (mt) REVERT: E 201 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8060 (tp) REVERT: E 442 LEU cc_start: 0.6995 (mm) cc_final: 0.6369 (mm) REVERT: E 445 MET cc_start: 0.5585 (mmm) cc_final: 0.5382 (mmp) REVERT: F 445 MET cc_start: 0.6967 (mtp) cc_final: 0.6558 (mtt) REVERT: G 19 ARG cc_start: 0.6166 (mtm-85) cc_final: 0.5778 (mtt-85) REVERT: G 23 LYS cc_start: 0.6759 (mttp) cc_final: 0.6383 (mtmt) REVERT: G 71 ASP cc_start: 0.3100 (t0) cc_final: 0.1933 (m-30) REVERT: H 63 MET cc_start: 0.4395 (ttm) cc_final: 0.4030 (mtp) REVERT: H 90 MET cc_start: 0.6672 (tmm) cc_final: 0.6393 (ttp) REVERT: H 104 LEU cc_start: 0.4725 (mt) cc_final: 0.4395 (mm) REVERT: J 85 ARG cc_start: 0.4913 (mmm160) cc_final: 0.4031 (tpp80) REVERT: K 113 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5654 (tt) REVERT: L 184 GLN cc_start: 0.5902 (pp30) cc_final: 0.5165 (tp40) outliers start: 56 outliers final: 32 residues processed: 359 average time/residue: 0.2112 time to fit residues: 117.3909 Evaluate side-chains 294 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 281 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 307 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 166 GLN ** F 323 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 = 0.3658 r_free = 0.3658 target = 0.125081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102755 restraints weight = 49521.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101915 restraints weight = 77360.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103155 restraints weight = 66908.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103306 restraints weight = 44751.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103434 restraints weight = 38857.407| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30112 Z= 0.123 Angle : 0.539 8.997 40807 Z= 0.275 Chirality : 0.043 0.188 4576 Planarity : 0.005 0.106 5333 Dihedral : 5.244 84.891 4209 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.43 % Allowed : 11.94 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.31 (0.14), residues: 3764 helix: 1.01 (0.13), residues: 1563 sheet: -0.87 (0.21), residues: 567 loop : -0.02 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 72 TYR 0.012 0.001 TYR G 133 PHE 0.015 0.001 PHE F 414 TRP 0.015 0.001 TRP B 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (30110) covalent geometry : angle 0.53885 / 0.27 (40807) hydrogen bonds : bond 0.03997 / 2.70 ( 1285) hydrogen bonds : angle 4.62876 / 3.20 ( 3702) Misc. bond : bond 0.00129 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 ASP cc_start: 0.7095 (p0) cc_final: 0.6569 (p0) REVERT: B 408 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6761 (tpp-160) REVERT: B 417 ARG cc_start: 0.6599 (mmp-170) cc_final: 0.5839 (mmm-85) REVERT: B 424 TRP cc_start: 0.6981 (p90) cc_final: 0.6683 (p90) REVERT: B 458 LEU cc_start: 0.7416 (mm) cc_final: 0.7045 (mt) REVERT: C 518 MET cc_start: 0.6476 (mtt) cc_final: 0.6142 (mtm) REVERT: D 419 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7842 (mt-10) REVERT: E 442 LEU cc_start: 0.6902 (mm) cc_final: 0.6319 (mm) REVERT: F 445 MET cc_start: 0.6854 (mtp) cc_final: 0.6404 (mtt) REVERT: G 19 ARG cc_start: 0.6105 (mtm-85) cc_final: 0.5651 (mtt-85) REVERT: G 23 LYS cc_start: 0.6667 (mttp) cc_final: 0.6298 (mtmt) REVERT: G 71 ASP cc_start: 0.3258 (t0) cc_final: 0.2138 (m-30) REVERT: H 63 MET cc_start: 0.4160 (ttm) cc_final: 0.3913 (mtp) REVERT: H 90 MET cc_start: 0.6761 (tmm) cc_final: 0.6272 (ttp) outliers start: 44 outliers final: 25 residues processed: 314 average time/residue: 0.1919 time to fit residues: 96.9829 Evaluate side-chains 267 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 280 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 260 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101223 restraints weight = 49567.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100207 restraints weight = 75767.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101159 restraints weight = 66108.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101597 restraints weight = 44471.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101659 restraints weight = 40338.421| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30112 Z= 0.181 Angle : 0.577 9.309 40807 Z= 0.292 Chirality : 0.045 0.176 4576 Planarity : 0.005 0.055 5333 Dihedral : 5.255 84.691 4209 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.24 % Allowed : 12.91 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.23 (0.14), residues: 3764 helix: 1.00 (0.13), residues: 1561 sheet: -1.01 (0.21), residues: 585 loop : -0.07 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 72 TYR 0.015 0.002 TYR F 13 PHE 0.019 0.002 PHE B 415 TRP 0.013 0.001 TRP F 471 HIS 0.005 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (30110) covalent geometry : angle 0.57716 / 0.29 (40807) hydrogen bonds : bond 0.04151 / 2.79 ( 1285) hydrogen bonds : angle 4.61826 / 3.19 ( 3702) Misc. bond : bond 0.00171 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6844 (tp30) cc_final: 0.6560 (tp30) REVERT: A 239 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: B 128 GLU cc_start: 0.7256 (tp30) cc_final: 0.7003 (tp30) REVERT: B 282 MET cc_start: 0.7878 (mmt) cc_final: 0.7647 (mmt) REVERT: B 408 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.6713 (tpp-160) REVERT: B 417 ARG cc_start: 0.6579 (mmp-170) cc_final: 0.5827 (mmm-85) REVERT: B 424 TRP cc_start: 0.7128 (p90) cc_final: 0.6899 (p90) REVERT: B 458 LEU cc_start: 0.7423 (mm) cc_final: 0.7072 (mt) REVERT: B 485 GLU cc_start: 0.5395 (mm-30) cc_final: 0.5188 (mm-30) REVERT: B 520 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.5008 (mm) REVERT: C 294 MET cc_start: 0.8073 (mtt) cc_final: 0.7773 (mtt) REVERT: C 485 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7131 (mm-30) REVERT: D 419 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7917 (mt-10) REVERT: E 22 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7070 (mm-30) REVERT: E 57 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8651 (mt) REVERT: E 201 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7998 (tt) REVERT: F 445 MET cc_start: 0.6958 (mtp) cc_final: 0.6545 (mtt) REVERT: G 19 ARG cc_start: 0.6069 (mtm-85) cc_final: 0.5661 (mtt-85) REVERT: G 71 ASP cc_start: 0.3426 (t0) cc_final: 0.2178 (m-30) REVERT: H 90 MET cc_start: 0.6755 (tmm) cc_final: 0.6277 (ttp) REVERT: J 74 GLN cc_start: 0.6311 (tm-30) cc_final: 0.4466 (pt0) REVERT: K 87 ARG cc_start: 0.4189 (OUTLIER) cc_final: 0.3275 (tpt90) outliers start: 69 outliers final: 43 residues processed: 311 average time/residue: 0.1807 time to fit residues: 91.5409 Evaluate side-chains 289 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 39 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 6 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 348 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102964 restraints weight = 49426.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102198 restraints weight = 70472.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103121 restraints weight = 61152.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103520 restraints weight = 40775.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103623 restraints weight = 36552.505| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30112 Z= 0.127 Angle : 0.524 8.873 40807 Z= 0.265 Chirality : 0.043 0.177 4576 Planarity : 0.004 0.051 5333 Dihedral : 5.073 85.579 4209 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 14.21 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.34 (0.14), residues: 3764 helix: 1.16 (0.13), residues: 1560 sheet: -1.05 (0.21), residues: 576 loop : -0.06 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 409 TYR 0.013 0.001 TYR H 89 PHE 0.017 0.001 PHE B 415 TRP 0.012 0.001 TRP C 119 HIS 0.003 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (30110) covalent geometry : angle 0.52423 / 0.26 (40807) hydrogen bonds : bond 0.03760 / 2.53 ( 1285) hydrogen bonds : angle 4.49248 / 3.10 ( 3702) Misc. bond : bond 0.00116 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 85 ASP cc_start: 0.7116 (p0) cc_final: 0.6681 (p0) REVERT: B 128 GLU cc_start: 0.7128 (tp30) cc_final: 0.6870 (tp30) REVERT: B 282 MET cc_start: 0.7910 (mmt) cc_final: 0.7694 (mmt) REVERT: B 408 ARG cc_start: 0.6920 (ttm-80) cc_final: 0.6704 (tpp-160) REVERT: B 417 ARG cc_start: 0.6529 (mmp-170) cc_final: 0.5808 (mmm-85) REVERT: B 458 LEU cc_start: 0.7429 (mm) cc_final: 0.7048 (mt) REVERT: B 485 GLU cc_start: 0.5315 (mm-30) cc_final: 0.5073 (mm-30) REVERT: B 520 LEU cc_start: 0.5244 (OUTLIER) cc_final: 0.4954 (mm) REVERT: D 268 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7538 (ttt180) REVERT: D 419 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7910 (mt-10) REVERT: E 3 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6919 (pt) REVERT: E 22 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7044 (mm-30) REVERT: E 57 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8640 (mt) REVERT: E 201 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7990 (tt) REVERT: F 445 MET cc_start: 0.6982 (mtp) cc_final: 0.6558 (mtt) REVERT: G 19 ARG cc_start: 0.5970 (mtm-85) cc_final: 0.5641 (mtt-85) REVERT: G 71 ASP cc_start: 0.3557 (t0) cc_final: 0.2316 (m-30) REVERT: G 207 GLU cc_start: 0.1834 (OUTLIER) cc_final: 0.1573 (tp30) REVERT: J 74 GLN cc_start: 0.6312 (tm-30) cc_final: 0.4450 (pt0) REVERT: J 134 LEU cc_start: 0.2827 (OUTLIER) cc_final: 0.2537 (mp) REVERT: J 137 GLU cc_start: 0.4722 (mt-10) cc_final: 0.4468 (tt0) REVERT: K 87 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.3399 (tpt90) outliers start: 70 outliers final: 44 residues processed: 313 average time/residue: 0.1714 time to fit residues: 88.3725 Evaluate side-chains 292 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 119 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 0.8980 chunk 236 optimal weight: 0.6980 chunk 283 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 353 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN F 222 ASN ** F 323 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 = 0.3630 r_free = 0.3630 target = 0.123083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101761 restraints weight = 49479.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100819 restraints weight = 73746.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101742 restraints weight = 63706.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102182 restraints weight = 41772.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102268 restraints weight = 38229.749| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 30112 Z= 0.194 Angle : 0.583 8.902 40807 Z= 0.295 Chirality : 0.045 0.174 4576 Planarity : 0.005 0.054 5333 Dihedral : 5.213 83.717 4209 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.72 % Allowed : 14.76 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.16 (0.14), residues: 3764 helix: 1.00 (0.13), residues: 1562 sheet: -1.13 (0.21), residues: 538 loop : -0.19 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 547 TYR 0.019 0.002 TYR H 89 PHE 0.021 0.002 PHE B 415 TRP 0.013 0.001 TRP F 471 HIS 0.015 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (30110) covalent geometry : angle 0.58341 / 0.29 (40807) hydrogen bonds : bond 0.04182 / 2.81 ( 1285) hydrogen bonds : angle 4.61647 / 3.20 ( 3702) Misc. bond : bond 0.00171 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 251 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6886 (tp30) cc_final: 0.6686 (tp30) REVERT: A 570 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6463 (mt) REVERT: B 85 ASP cc_start: 0.7174 (p0) cc_final: 0.6700 (p0) REVERT: B 128 GLU cc_start: 0.7145 (tp30) cc_final: 0.6920 (tp30) REVERT: B 408 ARG cc_start: 0.7008 (ttm-80) cc_final: 0.6738 (tpp-160) REVERT: B 417 ARG cc_start: 0.6587 (mmp-170) cc_final: 0.5883 (mmm-85) REVERT: B 458 LEU cc_start: 0.7388 (mm) cc_final: 0.7170 (mp) REVERT: B 520 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4952 (mm) REVERT: C 518 MET cc_start: 0.6537 (mtt) cc_final: 0.6140 (mtm) REVERT: D 268 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7608 (ttt180) REVERT: D 419 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7971 (mt-10) REVERT: E 3 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6932 (pt) REVERT: E 22 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7014 (mm-30) REVERT: E 57 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8649 (mt) REVERT: E 201 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 445 MET cc_start: 0.5595 (mmt) cc_final: 0.5380 (mmm) REVERT: F 445 MET cc_start: 0.7114 (mtp) cc_final: 0.6743 (mtt) REVERT: G 19 ARG cc_start: 0.5898 (mtm-85) cc_final: 0.5569 (mtt-85) REVERT: G 71 ASP cc_start: 0.3798 (t0) cc_final: 0.2563 (m-30) REVERT: G 207 GLU cc_start: 0.1953 (OUTLIER) cc_final: 0.1635 (tp30) REVERT: I 104 MET cc_start: 0.4551 (mmp) cc_final: 0.4219 (mmp) REVERT: J 74 GLN cc_start: 0.6306 (tm-30) cc_final: 0.4579 (pt0) REVERT: J 134 LEU cc_start: 0.2916 (OUTLIER) cc_final: 0.2662 (mp) REVERT: J 137 GLU cc_start: 0.4793 (mt-10) cc_final: 0.4537 (tt0) REVERT: K 87 ARG cc_start: 0.4357 (OUTLIER) cc_final: 0.3462 (tpt90) outliers start: 84 outliers final: 55 residues processed: 311 average time/residue: 0.1775 time to fit residues: 89.0832 Evaluate side-chains 302 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 276 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 213 optimal weight: 0.2980 chunk 168 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103797 restraints weight = 49316.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102995 restraints weight = 72570.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103919 restraints weight = 58221.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104249 restraints weight = 41251.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104385 restraints weight = 37066.623| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30112 Z= 0.102 Angle : 0.504 8.791 40807 Z= 0.254 Chirality : 0.043 0.177 4576 Planarity : 0.004 0.054 5333 Dihedral : 4.831 84.712 4209 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.62 % Allowed : 15.96 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.40 (0.14), residues: 3764 helix: 1.27 (0.13), residues: 1567 sheet: -1.10 (0.21), residues: 544 loop : -0.09 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 409 TYR 0.027 0.001 TYR H 89 PHE 0.013 0.001 PHE F 414 TRP 0.013 0.001 TRP J 175 HIS 0.008 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (30110) covalent geometry : angle 0.50353 / 0.25 (40807) hydrogen bonds : bond 0.03464 / 2.33 ( 1285) hydrogen bonds : angle 4.38583 / 3.03 ( 3702) Misc. bond : bond 0.00083 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6641 (t80) REVERT: B 393 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.5909 (mm-30) REVERT: B 408 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6760 (tpp-160) REVERT: B 417 ARG cc_start: 0.6459 (mmp-170) cc_final: 0.5774 (mmm-85) REVERT: B 458 LEU cc_start: 0.7380 (mm) cc_final: 0.6915 (mp) REVERT: B 520 LEU cc_start: 0.5115 (OUTLIER) cc_final: 0.4853 (mm) REVERT: C 518 MET cc_start: 0.6493 (mtt) cc_final: 0.6130 (mtm) REVERT: D 268 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7397 (ttt180) REVERT: E 22 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6989 (mm-30) REVERT: E 136 SER cc_start: 0.7569 (p) cc_final: 0.7337 (m) REVERT: E 416 ASP cc_start: 0.5893 (m-30) cc_final: 0.5533 (t0) REVERT: E 445 MET cc_start: 0.5545 (mmt) cc_final: 0.5244 (mmm) REVERT: F 409 ARG cc_start: 0.7000 (ttm110) cc_final: 0.6798 (mtp85) REVERT: F 445 MET cc_start: 0.7023 (mtp) cc_final: 0.6635 (mtt) REVERT: G 19 ARG cc_start: 0.5902 (mtm-85) cc_final: 0.5557 (mtt-85) REVERT: G 23 LYS cc_start: 0.6702 (mttp) cc_final: 0.6300 (mtmt) REVERT: G 71 ASP cc_start: 0.3906 (t0) cc_final: 0.2671 (m-30) REVERT: G 207 GLU cc_start: 0.1981 (OUTLIER) cc_final: 0.1659 (tp30) REVERT: I 104 MET cc_start: 0.4434 (mmp) cc_final: 0.4173 (mmp) REVERT: J 74 GLN cc_start: 0.6255 (tm-30) cc_final: 0.4477 (pt0) REVERT: J 137 GLU cc_start: 0.4869 (mt-10) cc_final: 0.4613 (tt0) REVERT: K 87 ARG cc_start: 0.4642 (OUTLIER) cc_final: 0.3623 (tpt90) outliers start: 50 outliers final: 28 residues processed: 306 average time/residue: 0.1790 time to fit residues: 89.8779 Evaluate side-chains 272 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain K residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 240 optimal weight: 5.9990 chunk 333 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102761 restraints weight = 49586.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102073 restraints weight = 70899.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103108 restraints weight = 57998.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103336 restraints weight = 39228.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103560 restraints weight = 37704.015| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30112 Z= 0.155 Angle : 0.548 8.775 40807 Z= 0.276 Chirality : 0.044 0.331 4576 Planarity : 0.005 0.065 5333 Dihedral : 4.930 84.615 4209 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.11 % Allowed : 15.50 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.32 (0.14), residues: 3764 helix: 1.17 (0.13), residues: 1564 sheet: -1.12 (0.21), residues: 537 loop : -0.11 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 547 TYR 0.032 0.001 TYR H 89 PHE 0.022 0.002 PHE B 494 TRP 0.011 0.001 TRP F 471 HIS 0.009 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (30110) covalent geometry : angle 0.54823 / 0.28 (40807) hydrogen bonds : bond 0.03788 / 2.55 ( 1285) hydrogen bonds : angle 4.43425 / 3.05 ( 3702) Misc. bond : bond 0.00138 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 256 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6914 (tp30) cc_final: 0.6398 (tp30) REVERT: A 574 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6530 (t80) REVERT: B 85 ASP cc_start: 0.7062 (p0) cc_final: 0.6581 (p0) REVERT: B 393 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5884 (mm-30) REVERT: B 408 ARG cc_start: 0.6985 (ttm-80) cc_final: 0.6725 (tpp-160) REVERT: B 417 ARG cc_start: 0.6588 (mmp-170) cc_final: 0.5884 (mmm-85) REVERT: B 458 LEU cc_start: 0.7395 (mm) cc_final: 0.7103 (mt) REVERT: B 520 LEU cc_start: 0.5144 (OUTLIER) cc_final: 0.4703 (mm) REVERT: D 268 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7592 (ttt180) REVERT: E 3 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6916 (pt) REVERT: E 22 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6988 (mm-30) REVERT: E 57 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8636 (mt) REVERT: E 136 SER cc_start: 0.7591 (p) cc_final: 0.7339 (m) REVERT: E 445 MET cc_start: 0.5631 (mmt) cc_final: 0.5345 (mmm) REVERT: F 409 ARG cc_start: 0.7011 (ttm110) cc_final: 0.6780 (mtp85) REVERT: F 445 MET cc_start: 0.7082 (mtp) cc_final: 0.6741 (mtt) REVERT: G 19 ARG cc_start: 0.5910 (mtm-85) cc_final: 0.5552 (mtt-85) REVERT: G 23 LYS cc_start: 0.6733 (mttp) cc_final: 0.6355 (mtmt) REVERT: G 71 ASP cc_start: 0.3913 (t0) cc_final: 0.2708 (m-30) REVERT: G 207 GLU cc_start: 0.1958 (OUTLIER) cc_final: 0.1667 (tp30) REVERT: H 90 MET cc_start: 0.6258 (tmm) cc_final: 0.5845 (ttp) REVERT: I 104 MET cc_start: 0.4464 (mmp) cc_final: 0.4182 (mmp) REVERT: J 134 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2713 (mp) REVERT: J 137 GLU cc_start: 0.4805 (mt-10) cc_final: 0.4604 (tt0) REVERT: K 87 ARG cc_start: 0.4720 (OUTLIER) cc_final: 0.3684 (tpt90) outliers start: 65 outliers final: 46 residues processed: 305 average time/residue: 0.1766 time to fit residues: 88.6537 Evaluate side-chains 299 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 175 optimal weight: 2.9990 chunk 364 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 305 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 341 optimal weight: 0.0270 chunk 301 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101744 restraints weight = 49536.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100479 restraints weight = 65274.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101154 restraints weight = 57873.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101782 restraints weight = 45759.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101852 restraints weight = 40027.325| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30112 Z= 0.178 Angle : 0.573 9.859 40807 Z= 0.290 Chirality : 0.045 0.278 4576 Planarity : 0.005 0.056 5333 Dihedral : 5.059 82.233 4209 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.34 % Allowed : 15.83 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.17 (0.14), residues: 3764 helix: 1.04 (0.13), residues: 1563 sheet: -1.21 (0.21), residues: 537 loop : -0.18 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 132 TYR 0.025 0.002 TYR H 89 PHE 0.016 0.002 PHE B 494 TRP 0.013 0.001 TRP F 471 HIS 0.009 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (30110) covalent geometry : angle 0.57321 / 0.29 (40807) hydrogen bonds : bond 0.04013 / 2.71 ( 1285) hydrogen bonds : angle 4.51791 / 3.11 ( 3702) Misc. bond : bond 0.00150 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 244 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6559 (t80) REVERT: B 85 ASP cc_start: 0.7067 (p0) cc_final: 0.6708 (p0) REVERT: B 393 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5889 (mm-30) REVERT: B 408 ARG cc_start: 0.6979 (ttm-80) cc_final: 0.6727 (tpp-160) REVERT: B 417 ARG cc_start: 0.6566 (mmp-170) cc_final: 0.5786 (mmm-85) REVERT: B 458 LEU cc_start: 0.7398 (mm) cc_final: 0.7086 (mt) REVERT: B 520 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4818 (mm) REVERT: C 15 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9059 (mm) REVERT: C 518 MET cc_start: 0.6572 (mtt) cc_final: 0.6180 (mtm) REVERT: D 268 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7620 (ttt180) REVERT: E 3 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6856 (pt) REVERT: E 22 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6989 (mm-30) REVERT: E 57 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8642 (mt) REVERT: E 136 SER cc_start: 0.7576 (p) cc_final: 0.7357 (m) REVERT: E 201 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 445 MET cc_start: 0.5587 (mmt) cc_final: 0.5321 (mmm) REVERT: F 409 ARG cc_start: 0.6999 (ttm110) cc_final: 0.6772 (mtp85) REVERT: F 445 MET cc_start: 0.7129 (mtp) cc_final: 0.6777 (mtt) REVERT: G 19 ARG cc_start: 0.5884 (mtm-85) cc_final: 0.5584 (mtt-85) REVERT: G 23 LYS cc_start: 0.6765 (mttp) cc_final: 0.6368 (mtmt) REVERT: G 71 ASP cc_start: 0.4298 (t0) cc_final: 0.3025 (m-30) REVERT: G 207 GLU cc_start: 0.1925 (OUTLIER) cc_final: 0.1574 (tp30) REVERT: H 90 MET cc_start: 0.6333 (tmm) cc_final: 0.5948 (ttp) REVERT: I 104 MET cc_start: 0.4302 (mmp) cc_final: 0.4051 (mmp) REVERT: J 74 GLN cc_start: 0.6211 (tm-30) cc_final: 0.4345 (pt0) REVERT: J 134 LEU cc_start: 0.3032 (OUTLIER) cc_final: 0.2764 (mp) REVERT: J 137 GLU cc_start: 0.4998 (mt-10) cc_final: 0.4717 (tt0) REVERT: J 162 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6798 (pt0) REVERT: K 87 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.3733 (tpt90) outliers start: 72 outliers final: 47 residues processed: 300 average time/residue: 0.1771 time to fit residues: 87.3147 Evaluate side-chains 292 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 270 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 104 optimal weight: 0.0010 chunk 192 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102684 restraints weight = 49399.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101933 restraints weight = 68978.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102802 restraints weight = 59916.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103229 restraints weight = 41251.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103261 restraints weight = 37753.363| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30112 Z= 0.132 Angle : 0.537 10.536 40807 Z= 0.270 Chirality : 0.043 0.245 4576 Planarity : 0.004 0.053 5333 Dihedral : 4.933 82.028 4209 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.95 % Allowed : 16.35 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.27 (0.14), residues: 3764 helix: 1.15 (0.13), residues: 1564 sheet: -1.21 (0.21), residues: 538 loop : -0.14 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 132 TYR 0.038 0.001 TYR H 89 PHE 0.017 0.001 PHE B 494 TRP 0.012 0.001 TRP F 471 HIS 0.008 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (30110) covalent geometry : angle 0.53684 / 0.27 (40807) hydrogen bonds : bond 0.03721 / 2.51 ( 1285) hydrogen bonds : angle 4.43535 / 3.04 ( 3702) Misc. bond : bond 0.00116 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6764 (tp30) cc_final: 0.6522 (tp30) REVERT: A 574 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6616 (t80) REVERT: B 393 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5857 (mm-30) REVERT: B 408 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6744 (tpp-160) REVERT: B 417 ARG cc_start: 0.6523 (mmp-170) cc_final: 0.5812 (mmm-85) REVERT: B 458 LEU cc_start: 0.7429 (mm) cc_final: 0.7111 (mt) REVERT: B 485 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7094 (tt0) REVERT: B 520 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4699 (mm) REVERT: C 15 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9022 (mm) REVERT: C 518 MET cc_start: 0.6589 (mtt) cc_final: 0.6215 (mtm) REVERT: D 268 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7468 (ttt180) REVERT: E 3 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6896 (pt) REVERT: E 22 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6970 (mm-30) REVERT: E 57 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8653 (mt) REVERT: E 136 SER cc_start: 0.7575 (p) cc_final: 0.7351 (m) REVERT: F 409 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6753 (mtp85) REVERT: F 445 MET cc_start: 0.7068 (mtp) cc_final: 0.6696 (mtt) REVERT: G 19 ARG cc_start: 0.5865 (mtm-85) cc_final: 0.5568 (mtt-85) REVERT: G 71 ASP cc_start: 0.4198 (t0) cc_final: 0.2935 (m-30) REVERT: G 207 GLU cc_start: 0.1968 (OUTLIER) cc_final: 0.1642 (tp30) REVERT: H 90 MET cc_start: 0.6284 (tmm) cc_final: 0.5841 (ttp) REVERT: I 104 MET cc_start: 0.4462 (mmp) cc_final: 0.4208 (mmp) REVERT: J 74 GLN cc_start: 0.6206 (tm-30) cc_final: 0.4277 (pt0) REVERT: J 134 LEU cc_start: 0.3013 (OUTLIER) cc_final: 0.2750 (mp) REVERT: J 137 GLU cc_start: 0.5012 (mt-10) cc_final: 0.4769 (tt0) REVERT: J 162 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: K 87 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.3770 (tpt90) outliers start: 60 outliers final: 43 residues processed: 288 average time/residue: 0.1854 time to fit residues: 87.4706 Evaluate side-chains 291 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 267 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 362 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 356 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102465 restraints weight = 49644.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102049 restraints weight = 65124.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102964 restraints weight = 56046.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103161 restraints weight = 39419.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103283 restraints weight = 39162.463| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30112 Z= 0.153 Angle : 0.552 11.315 40807 Z= 0.278 Chirality : 0.044 0.233 4576 Planarity : 0.004 0.053 5333 Dihedral : 4.977 82.185 4209 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.14 % Allowed : 16.32 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.23 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1561 sheet: -1.20 (0.21), residues: 537 loop : -0.17 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 132 TYR 0.040 0.001 TYR H 89 PHE 0.015 0.001 PHE B 494 TRP 0.012 0.001 TRP F 471 HIS 0.008 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (30110) covalent geometry : angle 0.55228 / 0.28 (40807) hydrogen bonds : bond 0.03830 / 2.59 ( 1285) hydrogen bonds : angle 4.45929 / 3.06 ( 3702) Misc. bond : bond 0.00131 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.26 seconds wall clock time: 74 minutes 14.29 seconds (4454.29 seconds total)