Starting phenix.real_space_refine on Fri Feb 16 05:12:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3a_29690/02_2024/8g3a_29690_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3a_29690/02_2024/8g3a_29690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3a_29690/02_2024/8g3a_29690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3a_29690/02_2024/8g3a_29690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3a_29690/02_2024/8g3a_29690_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3a_29690/02_2024/8g3a_29690_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 9385 2.51 5 N 2374 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.77, per 1000 atoms: 0.54 Number of scatterers: 14442 At special positions: 0 Unit cell: (106.384, 116.848, 199.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 2619 8.00 N 2374 7.00 C 9385 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 11 sheets defined 55.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 removed outlier: 3.743A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.074A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.518A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.666A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.955A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 124 removed outlier: 3.598A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.651A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 removed outlier: 3.802A pdb=" N VAL A 154 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 176 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.562A pdb=" N SER A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.763A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 4.021A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.112A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.867A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.604A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.688A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 519 through 556 removed outlier: 3.747A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 571 through 604 removed outlier: 4.065A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 4.167A pdb=" N SER A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 643 removed outlier: 4.680A pdb=" N SER A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.836A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.744A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.085A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.920A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.574A pdb=" N GLN C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.573A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 13 through 28 Processing helix chain 'D' and resid 35 through 60 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 85 through 137 removed outlier: 3.871A pdb=" N MET D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 143 through 170 removed outlier: 4.467A pdb=" N SER D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 265 through 270 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 291 through 301 removed outlier: 3.579A pdb=" N ALA D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 325 through 333 removed outlier: 4.086A pdb=" N HIS D 330 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 29 removed outlier: 3.999A pdb=" N ALA E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 60 removed outlier: 4.065A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.762A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 137 Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 144 through 170 removed outlier: 4.395A pdb=" N SER E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 201 Processing helix chain 'E' and resid 218 through 234 Processing helix chain 'E' and resid 265 through 270 Proline residue: E 269 - end of helix No H-bonds generated for 'chain 'E' and resid 265 through 270' Processing helix chain 'E' and resid 282 through 285 Processing helix chain 'E' and resid 291 through 301 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 325 through 332 removed outlier: 3.939A pdb=" N HIS E 330 " --> pdb=" O GLN E 327 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE E 332 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.591A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 388 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.619A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= D, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.581A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 9 through 11 removed outlier: 8.039A pdb=" N LYS B 11 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS B 24 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 37 through 40 Processing sheet with id= G, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.702A pdb=" N ILE C 164 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE C 90 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE C 166 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR C 196 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA C 167 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 198 " --> pdb=" O ALA C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 179 through 182 Processing sheet with id= I, first strand: chain 'D' and resid 204 through 209 Processing sheet with id= J, first strand: chain 'E' and resid 178 through 182 removed outlier: 3.748A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 205 through 209 removed outlier: 7.134A pdb=" N ILE E 241 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLN E 208 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 243 " --> pdb=" O GLN E 208 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1983 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: 4.18 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2342 1.32 - 1.44: 3764 1.44 - 1.56: 8463 1.56 - 1.69: 26 1.69 - 1.81: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.462 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.461 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.608 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 98.33 - 109.20: 794 109.20 - 120.06: 12707 120.06 - 130.92: 6222 130.92 - 141.79: 53 141.79 - 152.65: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 152.65 -25.09 3.00e+00 1.11e-01 7.00e+01 angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 152.26 -24.70 3.00e+00 1.11e-01 6.78e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 111.25 -17.30 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C39 6OU A 702 " pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " ideal model delta sigma weight residual 127.60 112.20 15.40 3.00e+00 1.11e-01 2.64e+01 angle pdb=" C39 6OU A 703 " pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " ideal model delta sigma weight residual 127.60 112.92 14.68 3.00e+00 1.11e-01 2.39e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 8606 33.00 - 66.00: 256 66.00 - 99.00: 35 99.00 - 132.00: 1 132.00 - 165.00: 3 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 212.33 47.33 165.00 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C21 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 85.49 -76.72 162.21 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual 301.00 157.38 143.62 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1884 0.054 - 0.108: 309 0.108 - 0.162: 51 0.162 - 0.216: 1 0.216 - 0.270: 1 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.62 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CB THR A 541 " pdb=" CA THR A 541 " pdb=" OG1 THR A 541 " pdb=" CG2 THR A 541 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " 0.177 2.00e-02 2.50e+03 1.38e-01 1.89e+02 pdb=" C11 OLA E 401 " -0.081 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " 0.081 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO E 129 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 84 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO E 85 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 85 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 85 " 0.020 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 138 2.65 - 3.21: 13058 3.21 - 3.78: 20613 3.78 - 4.34: 27407 4.34 - 4.90: 45933 Nonbonded interactions: 107149 Sorted by model distance: nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.088 2.440 nonbonded pdb=" OE2 GLU A 555 " pdb=" OH TYR A 637 " model vdw 2.210 2.440 nonbonded pdb=" NE2 GLN A 91 " pdb=" OG SER A 179 " model vdw 2.210 2.520 nonbonded pdb=" O SER A 125 " pdb=" OH TYR E 40 " model vdw 2.224 2.440 nonbonded pdb=" O ALA E 211 " pdb=" OG SER E 245 " model vdw 2.233 2.440 ... (remaining 107144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.450 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.600 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 0.005 0.138 14709 Z= 0.292 Angle : 0.720 25.093 19778 Z= 0.341 Chirality : 0.041 0.270 2246 Planarity : 0.004 0.138 2468 Dihedral : 15.963 165.000 5527 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.04 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1779 helix: 1.62 (0.17), residues: 1005 sheet: -0.22 (0.42), residues: 188 loop : -1.99 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 70 HIS 0.005 0.001 HIS A 596 PHE 0.024 0.001 PHE D 63 TYR 0.019 0.001 TYR A 314 ARG 0.002 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.493 Fit side-chains REVERT: A 332 MET cc_start: 0.6674 (ppp) cc_final: 0.5683 (ppp) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2420 time to fit residues: 54.6751 Evaluate side-chains 118 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS B 61 HIS C 86 HIS C 226 ASN D 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14709 Z= 0.224 Angle : 0.531 7.276 19778 Z= 0.279 Chirality : 0.041 0.170 2246 Planarity : 0.004 0.058 2468 Dihedral : 10.718 155.342 2018 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 0.83 % Allowed : 6.33 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1779 helix: 1.69 (0.18), residues: 996 sheet: -0.02 (0.43), residues: 181 loop : -1.92 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 70 HIS 0.007 0.001 HIS A 596 PHE 0.019 0.001 PHE A 529 TYR 0.013 0.001 TYR A 164 ARG 0.003 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.648 Fit side-chains REVERT: A 332 MET cc_start: 0.6810 (ppp) cc_final: 0.5626 (ppp) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.2314 time to fit residues: 47.4564 Evaluate side-chains 125 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 173 optimal weight: 9.9990 chunk 143 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS B 61 HIS C 65 HIS C 86 HIS C 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.077 14709 Z= 0.688 Angle : 0.786 8.407 19778 Z= 0.412 Chirality : 0.050 0.257 2246 Planarity : 0.005 0.058 2468 Dihedral : 11.209 161.322 2018 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 2.11 % Allowed : 11.00 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1779 helix: 0.93 (0.17), residues: 999 sheet: -0.63 (0.40), residues: 196 loop : -2.13 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 12 HIS 0.011 0.001 HIS A 596 PHE 0.031 0.003 PHE A 630 TYR 0.023 0.003 TYR E 43 ARG 0.005 0.001 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.648 Fit side-chains REVERT: A 265 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7835 (ttpt) REVERT: A 314 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: A 332 MET cc_start: 0.6796 (ppp) cc_final: 0.5496 (ppp) REVERT: D 1 MET cc_start: 0.7288 (mmm) cc_final: 0.6761 (mmt) outliers start: 33 outliers final: 25 residues processed: 134 average time/residue: 0.2551 time to fit residues: 51.4573 Evaluate side-chains 130 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN C 65 HIS C 86 HIS C 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14709 Z= 0.281 Angle : 0.571 7.957 19778 Z= 0.300 Chirality : 0.041 0.199 2246 Planarity : 0.004 0.056 2468 Dihedral : 10.564 159.214 2018 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.25 % Rotamer: Outliers : 1.66 % Allowed : 13.24 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1779 helix: 1.31 (0.17), residues: 994 sheet: -0.57 (0.41), residues: 194 loop : -2.08 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 613 HIS 0.004 0.001 HIS A 596 PHE 0.021 0.001 PHE A 529 TYR 0.012 0.001 TYR A 164 ARG 0.002 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.593 Fit side-chains REVERT: A 35 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8154 (m-10) REVERT: A 314 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: A 332 MET cc_start: 0.6745 (ppp) cc_final: 0.5483 (ppp) REVERT: D 1 MET cc_start: 0.7277 (mmm) cc_final: 0.6902 (mmt) REVERT: D 7 ILE cc_start: 0.8511 (tt) cc_final: 0.8210 (tt) REVERT: E 57 TYR cc_start: 0.7895 (t80) cc_final: 0.7652 (t80) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.2421 time to fit residues: 49.1875 Evaluate side-chains 128 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN C 65 HIS C 86 HIS C 226 ASN E 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 14709 Z= 0.136 Angle : 0.488 7.339 19778 Z= 0.256 Chirality : 0.039 0.168 2246 Planarity : 0.003 0.054 2468 Dihedral : 9.891 156.888 2018 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 1.54 % Allowed : 14.33 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1779 helix: 1.70 (0.18), residues: 990 sheet: -0.33 (0.42), residues: 191 loop : -2.02 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 613 HIS 0.014 0.001 HIS C 65 PHE 0.013 0.001 PHE A 529 TYR 0.008 0.001 TYR D 64 ARG 0.002 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.724 Fit side-chains REVERT: A 35 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8260 (m-10) REVERT: A 314 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: A 332 MET cc_start: 0.6750 (ppp) cc_final: 0.5566 (ppp) REVERT: A 574 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8016 (mp) REVERT: E 57 TYR cc_start: 0.7902 (t80) cc_final: 0.7515 (t80) outliers start: 24 outliers final: 14 residues processed: 139 average time/residue: 0.2248 time to fit residues: 49.3018 Evaluate side-chains 130 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 171 optimal weight: 0.0980 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 14709 Z= 0.150 Angle : 0.479 7.370 19778 Z= 0.250 Chirality : 0.039 0.164 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.727 156.480 2018 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.13 % Favored : 93.70 % Rotamer: Outliers : 1.28 % Allowed : 14.78 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1779 helix: 1.80 (0.18), residues: 990 sheet: -0.26 (0.42), residues: 191 loop : -1.97 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 613 HIS 0.002 0.000 HIS D 165 PHE 0.016 0.001 PHE A 529 TYR 0.015 0.001 TYR D 57 ARG 0.002 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.710 Fit side-chains REVERT: A 35 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: A 314 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6052 (m-80) REVERT: A 332 MET cc_start: 0.6744 (ppp) cc_final: 0.5569 (ppp) REVERT: A 574 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7979 (mp) outliers start: 20 outliers final: 15 residues processed: 133 average time/residue: 0.2341 time to fit residues: 48.8181 Evaluate side-chains 137 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 0.0050 chunk 78 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14709 Z= 0.154 Angle : 0.474 8.338 19778 Z= 0.246 Chirality : 0.039 0.154 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.432 155.410 2018 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.24 % Favored : 93.65 % Rotamer: Outliers : 1.54 % Allowed : 15.04 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1779 helix: 1.87 (0.17), residues: 993 sheet: -0.17 (0.41), residues: 200 loop : -1.93 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.002 0.000 HIS D 165 PHE 0.022 0.001 PHE A 351 TYR 0.020 0.001 TYR E 57 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.421 Fit side-chains REVERT: A 35 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: A 314 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: A 332 MET cc_start: 0.6831 (ppp) cc_final: 0.5684 (ppp) REVERT: A 574 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7971 (mp) REVERT: C 94 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.6137 (p90) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.2267 time to fit residues: 47.2459 Evaluate side-chains 140 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 0.2980 chunk 134 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14709 Z= 0.175 Angle : 0.483 8.751 19778 Z= 0.251 Chirality : 0.039 0.153 2246 Planarity : 0.003 0.051 2468 Dihedral : 9.357 155.151 2018 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 1.98 % Allowed : 14.84 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1779 helix: 1.89 (0.17), residues: 993 sheet: -0.13 (0.41), residues: 200 loop : -1.95 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 613 HIS 0.002 0.000 HIS A 596 PHE 0.019 0.001 PHE A 529 TYR 0.017 0.001 TYR E 57 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.652 Fit side-chains REVERT: A 35 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: A 314 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: A 332 MET cc_start: 0.6890 (ppp) cc_final: 0.5763 (ppp) REVERT: A 574 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8017 (mp) REVERT: C 94 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.5957 (p90) outliers start: 31 outliers final: 22 residues processed: 137 average time/residue: 0.2319 time to fit residues: 50.0263 Evaluate side-chains 143 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 30.0000 chunk 149 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14709 Z= 0.163 Angle : 0.482 9.102 19778 Z= 0.249 Chirality : 0.039 0.161 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.157 154.350 2018 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 1.86 % Allowed : 14.84 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1779 helix: 1.91 (0.17), residues: 993 sheet: -0.12 (0.43), residues: 191 loop : -1.91 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.002 0.000 HIS A 596 PHE 0.018 0.001 PHE A 351 TYR 0.017 0.001 TYR E 57 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.489 Fit side-chains REVERT: A 35 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: A 314 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6039 (m-80) REVERT: A 332 MET cc_start: 0.6847 (ppp) cc_final: 0.5714 (ppp) REVERT: A 574 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7983 (mp) REVERT: C 94 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.5841 (p90) outliers start: 29 outliers final: 23 residues processed: 137 average time/residue: 0.2249 time to fit residues: 48.4188 Evaluate side-chains 145 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.2980 chunk 162 optimal weight: 7.9990 chunk 140 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 61 HIS C 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14709 Z= 0.246 Angle : 0.531 9.671 19778 Z= 0.273 Chirality : 0.040 0.160 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.386 155.296 2018 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.75 % Favored : 93.14 % Rotamer: Outliers : 1.79 % Allowed : 14.84 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1779 helix: 1.78 (0.17), residues: 995 sheet: -0.25 (0.42), residues: 194 loop : -1.93 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 122 HIS 0.004 0.001 HIS B 61 PHE 0.022 0.001 PHE A 529 TYR 0.017 0.001 TYR E 57 ARG 0.002 0.000 ARG A 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.571 Fit side-chains REVERT: A 35 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8277 (m-10) REVERT: A 314 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: A 332 MET cc_start: 0.6770 (ppp) cc_final: 0.5676 (ppp) REVERT: A 574 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8102 (mp) outliers start: 28 outliers final: 24 residues processed: 134 average time/residue: 0.2284 time to fit residues: 47.9776 Evaluate side-chains 142 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 140 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.241508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.173075 restraints weight = 17980.135| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.58 r_work: 0.3232 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14709 Z= 0.193 Angle : 0.502 9.504 19778 Z= 0.259 Chirality : 0.040 0.164 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.227 154.260 2018 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.07 % Favored : 93.82 % Rotamer: Outliers : 1.79 % Allowed : 14.91 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1779 helix: 1.82 (0.17), residues: 993 sheet: -0.23 (0.42), residues: 194 loop : -1.89 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.003 0.000 HIS A 596 PHE 0.019 0.001 PHE A 529 TYR 0.016 0.001 TYR E 57 ARG 0.002 0.000 ARG E 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2961.90 seconds wall clock time: 54 minutes 43.87 seconds (3283.87 seconds total)