Starting phenix.real_space_refine on Thu Jul 2 19:29:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps5_71823/07_2026/9ps5_71823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps5_71823/07_2026/9ps5_71823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ps5_71823/07_2026/9ps5_71823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps5_71823/07_2026/9ps5_71823.map" model { file = "/net/cci-nas-00/data/ceres_data/9ps5_71823/07_2026/9ps5_71823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps5_71823/07_2026/9ps5_71823.cif" } resolution = 3.93 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= 0.002 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 6231 2.51 5 N 1612 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 9564 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3270 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 523 Unresolved non-hydrogen angles: 682 Unresolved non-hydrogen dihedrals: 433 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 10, 'ASN:plan1': 9, 'PHE:plan': 7, 'HIS:plan': 1, 'GLU:plan': 4, 'TYR:plan': 7, 'GLN:plan1': 4, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 259 Chain: "B" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3113 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 695 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 12, 'ASN:plan1': 8, 'PHE:plan': 13, 'HIS:plan': 3, 'GLU:plan': 5, 'TYR:plan': 7, 'TRP:plan': 5, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 344 Chain: "C" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3181 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 21, 'TRANS': 463} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 12, 'HIS:plan': 3, 'GLU:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 5, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 305 Time building chain proxies: 2.31, per 1000 atoms: 0.24 Number of scatterers: 9564 At special positions: 0 Unit cell: (124.7, 122.12, 78.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1690 8.00 N 1612 7.00 C 6231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 401.1 milliseconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 7 sheets defined 84.7% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 95 through 121 removed outlier: 4.091A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.519A pdb=" N LEU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 removed outlier: 4.090A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.692A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 removed outlier: 3.918A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 254 removed outlier: 3.535A pdb=" N GLN A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 313 through 320 removed outlier: 4.067A pdb=" N THR A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 374 removed outlier: 5.020A pdb=" N VAL A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 390 through 409 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 418 through 451 removed outlier: 3.842A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 436 " --> pdb=" O TRP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.556A pdb=" N TRP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 3.660A pdb=" N ALA A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 554 through 578 removed outlier: 4.122A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.764A pdb=" N ARG B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 121 removed outlier: 4.146A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 136 through 163 removed outlier: 4.346A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Proline residue: B 152 - end of helix removed outlier: 4.399A pdb=" N ASP B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.824A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 227 through 254 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.537A pdb=" N LEU B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 320 removed outlier: 3.846A pdb=" N THR B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 342 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 374 Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 389 through 409 Processing helix chain 'B' and resid 417 through 452 removed outlier: 3.780A pdb=" N PHE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 436 " --> pdb=" O TRP B 432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 461 Processing helix chain 'B' and resid 461 through 482 removed outlier: 4.723A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.767A pdb=" N ALA B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 554 through 577 removed outlier: 4.143A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 120 removed outlier: 3.527A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 143 through 162 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 163 through 193 removed outlier: 4.031A pdb=" N GLY C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 223 removed outlier: 3.636A pdb=" N PHE C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 254 Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 313 through 320 Processing helix chain 'C' and resid 321 through 342 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.769A pdb=" N VAL C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 389 through 408 Processing helix chain 'C' and resid 417 through 451 removed outlier: 3.978A pdb=" N PHE C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 481 removed outlier: 3.562A pdb=" N LEU C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 481 " --> pdb=" O THR C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 3.609A pdb=" N PHE C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 546 Processing helix chain 'C' and resid 547 through 550 Processing helix chain 'C' and resid 554 through 577 removed outlier: 4.083A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.891A pdb=" N PHE A 195 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 removed outlier: 4.325A pdb=" N ILE A 384 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.850A pdb=" N PHE B 195 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'C' and resid 195 through 196 removed outlier: 4.014A pdb=" N PHE C 195 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 553 " --> pdb=" O PHE C 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 226 864 hydrogen bonds defined for protein. 2562 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: 1.55 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2068 1.33 - 1.45: 2102 1.45 - 1.57: 5523 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 9733 Sorted by residual: bond pdb=" N LEU C 96 " pdb=" CA LEU C 96 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.04e+01 bond pdb=" N LEU C 95 " pdb=" CA LEU C 95 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.21e+00 bond pdb=" N ILE B 100 " pdb=" CA ILE B 100 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.86e+00 bond pdb=" N LEU B 95 " pdb=" CA LEU B 95 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.13e+00 bond pdb=" N THR C 373 " pdb=" CA THR C 373 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.28e-02 6.10e+03 6.75e+00 ... (remaining 9728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12974 1.65 - 3.30: 339 3.30 - 4.95: 48 4.95 - 6.60: 14 6.60 - 8.25: 6 Bond angle restraints: 13381 Sorted by residual: angle pdb=" N SER B 136 " pdb=" CA SER B 136 " pdb=" C SER B 136 " ideal model delta sigma weight residual 110.41 105.80 4.61 1.23e+00 6.61e-01 1.41e+01 angle pdb=" N LEU C 133 " pdb=" CA LEU C 133 " pdb=" C LEU C 133 " ideal model delta sigma weight residual 113.20 109.14 4.06 1.21e+00 6.83e-01 1.13e+01 angle pdb=" N TYR A 103 " pdb=" CA TYR A 103 " pdb=" C TYR A 103 " ideal model delta sigma weight residual 111.28 107.78 3.50 1.09e+00 8.42e-01 1.03e+01 angle pdb=" N ASN B 94 " pdb=" CA ASN B 94 " pdb=" C ASN B 94 " ideal model delta sigma weight residual 112.87 109.02 3.85 1.20e+00 6.94e-01 1.03e+01 angle pdb=" CA ILE B 100 " pdb=" C ILE B 100 " pdb=" O ILE B 100 " ideal model delta sigma weight residual 120.95 117.71 3.24 1.04e+00 9.25e-01 9.69e+00 ... (remaining 13376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5006 17.66 - 35.33: 400 35.33 - 52.99: 117 52.99 - 70.66: 8 70.66 - 88.32: 5 Dihedral angle restraints: 5536 sinusoidal: 1360 harmonic: 4176 Sorted by residual: dihedral pdb=" CA VAL B 364 " pdb=" C VAL B 364 " pdb=" N ILE B 365 " pdb=" CA ILE B 365 " ideal model delta harmonic sigma weight residual 180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR C 143 " pdb=" C THR C 143 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta harmonic sigma weight residual 180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL C 364 " pdb=" C VAL C 364 " pdb=" N ILE C 365 " pdb=" CA ILE C 365 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1228 0.042 - 0.084: 365 0.084 - 0.126: 99 0.126 - 0.169: 17 0.169 - 0.211: 3 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU B 95 " pdb=" N LEU B 95 " pdb=" C LEU B 95 " pdb=" CB LEU B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA LEU A 102 " pdb=" N LEU A 102 " pdb=" C LEU A 102 " pdb=" CB LEU A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 1709 not shown) Planarity restraints: 1700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 568 " -0.015 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE B 568 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 568 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 568 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 568 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 568 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 568 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 441 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C VAL C 441 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL C 441 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN C 442 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 535 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C LEU C 535 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU C 535 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY C 536 " -0.009 2.00e-02 2.50e+03 ... (remaining 1697 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 915 2.74 - 3.28: 10581 3.28 - 3.82: 16136 3.82 - 4.36: 15818 4.36 - 4.90: 27496 Nonbonded interactions: 70946 Sorted by model distance: nonbonded pdb=" O PHE B 239 " pdb=" OG1 THR B 243 " model vdw 2.199 3.040 nonbonded pdb=" ND2 ASN B 125 " pdb=" O ALA B 422 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR C 83 " pdb=" OE1 GLU C 439 " model vdw 2.260 3.040 nonbonded pdb=" O PHE A 426 " pdb=" OG SER A 429 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASN A 498 " pdb=" N ILE A 499 " model vdw 2.272 3.120 ... (remaining 70941 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 53 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 through 120 or (resid 121 through 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 or (resid 142 through 144 \ and (name N or name CA or name C or name O or name CB )) or resid 145 through 15 \ 4 or (resid 155 through 167 and (name N or name CA or name C or name O or name C \ B )) or resid 168 or (resid 169 through 171 and (name N or name CA or name C or \ name O or name CB )) or resid 172 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 230 or (resid 231 and \ (name N or name CA or name C or name O or name CB )) or resid 232 through 241 or \ (resid 242 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 3 through 245 or (resid 246 and (name N or name CA or name C or name O or name C \ B )) or resid 247 through 248 or (resid 249 and (name N or name CA or name C or \ name O or name CB )) or resid 250 through 252 or (resid 253 and (name N or name \ CA or name C or name O or name CB )) or resid 254 or (resid 300 through 301 and \ (name N or name CA or name C or name O or name CB )) or resid 302 or (resid 303 \ through 376 and (name N or name CA or name C or name O or name CB )) or (resid 3 \ 77 through 424 and (name N or name CA or name C or name O or name CB )) or resid \ 425 or (resid 426 through 447 and (name N or name CA or name C or name O or nam \ e CB )) or resid 448 through 512 or (resid 513 and (name N or name CA or name C \ or name O or name CB )) or resid 514 through 575 or (resid 576 through 577 and ( \ name N or name CA or name C or name O or name CB )) or resid 578 or (resid 579 t \ hrough 581 and (name N or name CA or name C or name O or name CB )) or resid 582 \ )) selection = (chain 'B' and (resid 53 through 120 or (resid 121 through 140 and (name N or na \ me CA or name C or name O or name CB )) or resid 141 or (resid 142 through 144 a \ nd (name N or name CA or name C or name O or name CB )) or resid 145 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB )) or resid 425 or (resid 426 through 447 and (name N or name CA or name C \ or name O or name CB )) or (resid 448 through 458 and (name N or name CA or name \ C or name O or name CB )) or resid 459 through 512 or (resid 513 and (name N or \ name CA or name C or name O or name CB )) or resid 514 through 582)) selection = (chain 'C' and ((resid 53 through 77 and (name N or name CA or name C or name O \ or name CB )) or (resid 78 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 or (resid 87 through 105 and (name N or name CA or na \ me C or name O or name CB )) or resid 106 through 154 or (resid 155 through 167 \ and (name N or name CA or name C or name O or name CB )) or resid 168 or (resid \ 169 through 171 and (name N or name CA or name C or name O or name CB )) or resi \ d 172 through 230 or (resid 231 and (name N or name CA or name C or name O or na \ me CB )) or resid 232 through 241 or (resid 242 and (name N or name CA or name C \ or name O or name CB )) or resid 243 through 245 or (resid 246 and (name N or n \ ame CA or name C or name O or name CB )) or resid 247 through 248 or (resid 249 \ and (name N or name CA or name C or name O or name CB )) or resid 250 through 25 \ 2 or (resid 253 and (name N or name CA or name C or name O or name CB )) or resi \ d 254 through 437 or (resid 438 through 447 and (name N or name CA or name C or \ name O or name CB )) or resid 448 or (resid 449 through 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 through 575 or (resid 576 thro \ ugh 577 and (name N or name CA or name C or name O or name CB )) or resid 578 or \ (resid 579 through 581 and (name N or name CA or name C or name O or name CB )) \ or resid 582)) } 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.420 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 0.039 9733 Z= 0.202 Angle : 0.655 8.250 13381 Z= 0.391 Chirality : 0.043 0.211 1712 Planarity : 0.004 0.027 1700 Dihedral : 14.880 88.319 2844 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.42 % Allowed : 33.57 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1445 helix: 0.66 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 193 TYR 0.012 0.001 TYR A 565 PHE 0.031 0.001 PHE B 568 TRP 0.007 0.001 TRP A 106 HIS 0.001 0.000 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 ( 9733) covalent geometry : angle 0.65523 / 0.39 (13381) hydrogen bonds : bond 0.16127 / 11.65 ( 864) hydrogen bonds : angle 6.73455 / 4.96 ( 2562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 205 ASP cc_start: 0.8859 (t70) cc_final: 0.8481 (t0) REVERT: A 471 ASP cc_start: 0.7826 (m-30) cc_final: 0.7533 (t70) REVERT: A 481 GLN cc_start: 0.8437 (mp10) cc_final: 0.7729 (mp10) REVERT: B 120 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8200 (mptt) REVERT: C 163 ASP cc_start: 0.7482 (t0) cc_final: 0.7185 (t0) REVERT: C 480 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7991 (ttm170) REVERT: C 507 CYS cc_start: 0.8903 (m) cc_final: 0.8295 (p) REVERT: C 552 GLN cc_start: 0.8967 (mm110) cc_final: 0.8756 (mm-40) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.0962 time to fit residues: 25.0665 Evaluate side-chains 143 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091248 restraints weight = 30485.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093765 restraints weight = 16104.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095246 restraints weight = 10458.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.096237 restraints weight = 7959.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096516 restraints weight = 6622.843| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9733 Z= 0.146 Angle : 0.581 10.331 13381 Z= 0.306 Chirality : 0.040 0.168 1712 Planarity : 0.003 0.023 1700 Dihedral : 4.104 42.972 1510 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 5.64 % Allowed : 30.89 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.22), residues: 1445 helix: 1.67 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.42 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 204 TYR 0.015 0.001 TYR A 240 PHE 0.023 0.001 PHE B 568 TRP 0.019 0.001 TRP A 106 HIS 0.003 0.000 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 9733) covalent geometry : angle 0.58145 / 0.31 (13381) hydrogen bonds : bond 0.04809 / 3.51 ( 864) hydrogen bonds : angle 4.45973 / 3.31 ( 2562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.372 Fit side-chains REVERT: A 205 ASP cc_start: 0.8795 (t0) cc_final: 0.8406 (t0) REVERT: A 462 LEU cc_start: 0.8719 (tt) cc_final: 0.8417 (mm) REVERT: A 520 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8163 (mmtt) REVERT: B 125 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8439 (t0) REVERT: B 481 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: B 497 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 518 GLU cc_start: 0.8227 (pp20) cc_final: 0.7802 (pp20) REVERT: B 549 GLN cc_start: 0.9054 (tt0) cc_final: 0.8830 (mt0) REVERT: B 567 CYS cc_start: 0.9284 (t) cc_final: 0.8980 (t) REVERT: C 89 CYS cc_start: 0.8877 (m) cc_final: 0.8299 (t) REVERT: C 439 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9183 (mm-30) REVERT: C 480 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7960 (ttm170) REVERT: C 507 CYS cc_start: 0.8996 (m) cc_final: 0.8328 (p) REVERT: C 510 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.8534 (tp40) REVERT: C 552 GLN cc_start: 0.8946 (mm110) cc_final: 0.8728 (mm-40) outliers start: 40 outliers final: 25 residues processed: 190 average time/residue: 0.0726 time to fit residues: 20.5602 Evaluate side-chains 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 77 optimal weight: 50.0000 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 121 optimal weight: 0.0050 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN ** B 549 GLN ** 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 = 0.3827 r_free = 0.3827 target = 0.118922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094564 restraints weight = 29932.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097190 restraints weight = 15465.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098579 restraints weight = 9843.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099727 restraints weight = 7536.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100174 restraints weight = 6150.242| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9733 Z= 0.126 Angle : 0.566 10.843 13381 Z= 0.291 Chirality : 0.040 0.155 1712 Planarity : 0.003 0.026 1700 Dihedral : 3.768 16.719 1508 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 6.35 % Allowed : 31.73 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.22), residues: 1445 helix: 2.05 (0.15), residues: 1141 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.012 0.001 TYR B 237 PHE 0.027 0.001 PHE B 568 TRP 0.015 0.001 TRP A 106 HIS 0.001 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 9733) covalent geometry : angle 0.56581 / 0.29 (13381) hydrogen bonds : bond 0.04182 / 3.04 ( 864) hydrogen bonds : angle 4.04827 / 3.01 ( 2562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 205 ASP cc_start: 0.8777 (t0) cc_final: 0.8439 (t0) REVERT: A 332 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 423 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: A 462 LEU cc_start: 0.8648 (tt) cc_final: 0.8394 (mm) REVERT: A 471 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7024 (t70) REVERT: A 510 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8703 (mm-40) REVERT: A 557 TYR cc_start: 0.8527 (t80) cc_final: 0.8270 (t80) REVERT: B 209 TYR cc_start: 0.9063 (t80) cc_final: 0.8861 (t80) REVERT: B 481 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: B 497 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 518 GLU cc_start: 0.8279 (pp20) cc_final: 0.7916 (pp20) REVERT: B 548 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (tp) REVERT: B 567 CYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8969 (t) REVERT: C 89 CYS cc_start: 0.8811 (m) cc_final: 0.8278 (t) REVERT: C 439 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9154 (mm-30) REVERT: C 480 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7889 (ttm170) REVERT: C 507 CYS cc_start: 0.9019 (m) cc_final: 0.8338 (p) REVERT: C 510 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8563 (tp40) REVERT: C 522 GLU cc_start: 0.8160 (tp30) cc_final: 0.7782 (mm-30) outliers start: 45 outliers final: 28 residues processed: 200 average time/residue: 0.0691 time to fit residues: 21.1500 Evaluate side-chains 190 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 61 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 29 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** B 549 GLN ** 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 = 0.3796 r_free = 0.3796 target = 0.116530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091849 restraints weight = 30415.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094367 restraints weight = 15826.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095749 restraints weight = 10204.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096803 restraints weight = 7826.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097101 restraints weight = 6451.112| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9733 Z= 0.144 Angle : 0.572 11.455 13381 Z= 0.294 Chirality : 0.040 0.178 1712 Planarity : 0.003 0.023 1700 Dihedral : 3.645 16.992 1508 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 7.76 % Allowed : 33.43 % Favored : 58.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.22), residues: 1445 helix: 2.29 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 204 TYR 0.018 0.001 TYR B 240 PHE 0.014 0.001 PHE B 568 TRP 0.013 0.001 TRP A 106 HIS 0.001 0.000 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9733) covalent geometry : angle 0.57224 / 0.29 (13381) hydrogen bonds : bond 0.04073 / 2.94 ( 864) hydrogen bonds : angle 3.88418 / 2.89 ( 2562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.8845 (t0) cc_final: 0.8593 (t70) REVERT: A 332 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 423 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8993 (m-80) REVERT: A 471 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7087 (t70) REVERT: A 510 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8672 (mm-40) REVERT: B 153 ASP cc_start: 0.8345 (t0) cc_final: 0.7573 (t0) REVERT: B 481 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: B 497 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8306 (t80) REVERT: B 518 GLU cc_start: 0.8353 (pp20) cc_final: 0.7998 (pp20) REVERT: B 548 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8960 (tp) REVERT: B 567 CYS cc_start: 0.9354 (t) cc_final: 0.9034 (t) REVERT: C 89 CYS cc_start: 0.8841 (m) cc_final: 0.8225 (t) REVERT: C 439 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9137 (mm-30) REVERT: C 475 ASP cc_start: 0.8654 (m-30) cc_final: 0.8403 (m-30) REVERT: C 480 ARG cc_start: 0.8240 (mmm160) cc_final: 0.8014 (ttm170) REVERT: C 507 CYS cc_start: 0.8998 (m) cc_final: 0.8333 (p) REVERT: C 522 GLU cc_start: 0.8153 (tp30) cc_final: 0.7808 (mm-30) outliers start: 55 outliers final: 38 residues processed: 194 average time/residue: 0.0690 time to fit residues: 20.6611 Evaluate side-chains 189 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 76 optimal weight: 40.0000 chunk 118 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 50.0000 chunk 13 optimal weight: 0.0070 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 549 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.116195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090864 restraints weight = 30530.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093360 restraints weight = 16175.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094750 restraints weight = 10492.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.095759 restraints weight = 8115.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096166 restraints weight = 6733.806| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9733 Z= 0.145 Angle : 0.572 11.123 13381 Z= 0.292 Chirality : 0.040 0.153 1712 Planarity : 0.003 0.025 1700 Dihedral : 3.606 16.863 1508 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 8.32 % Allowed : 33.57 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.22), residues: 1445 helix: 2.40 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 204 TYR 0.018 0.001 TYR B 240 PHE 0.016 0.001 PHE B 568 TRP 0.018 0.001 TRP A 106 HIS 0.001 0.000 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9733) covalent geometry : angle 0.57181 / 0.29 (13381) hydrogen bonds : bond 0.03978 / 2.88 ( 864) hydrogen bonds : angle 3.79547 / 2.83 ( 2562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 205 ASP cc_start: 0.8841 (t0) cc_final: 0.8585 (t70) REVERT: A 332 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 423 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.9021 (m-80) REVERT: A 471 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6935 (t0) REVERT: A 520 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8202 (mmmt) REVERT: A 557 TYR cc_start: 0.8778 (t80) cc_final: 0.8551 (t80) REVERT: B 209 TYR cc_start: 0.9148 (t80) cc_final: 0.8934 (t80) REVERT: B 210 MET cc_start: 0.9408 (tpp) cc_final: 0.9052 (mmm) REVERT: B 481 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: B 497 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8428 (t80) REVERT: B 518 GLU cc_start: 0.8406 (pp20) cc_final: 0.8024 (pp20) REVERT: B 548 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9001 (tp) REVERT: B 567 CYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9002 (t) REVERT: C 82 ASP cc_start: 0.8591 (t0) cc_final: 0.7908 (t0) REVERT: C 85 LYS cc_start: 0.8811 (mptt) cc_final: 0.8485 (mmtt) REVERT: C 89 CYS cc_start: 0.8808 (m) cc_final: 0.8208 (t) REVERT: C 475 ASP cc_start: 0.8630 (m-30) cc_final: 0.8328 (m-30) REVERT: C 507 CYS cc_start: 0.8954 (m) cc_final: 0.8341 (p) outliers start: 59 outliers final: 38 residues processed: 189 average time/residue: 0.0711 time to fit residues: 20.7307 Evaluate side-chains 185 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 40.0000 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091008 restraints weight = 30234.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.092447 restraints weight = 14078.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093210 restraints weight = 9251.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094341 restraints weight = 8461.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094376 restraints weight = 7336.095| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9733 Z= 0.181 Angle : 0.601 11.624 13381 Z= 0.311 Chirality : 0.041 0.153 1712 Planarity : 0.003 0.027 1700 Dihedral : 3.686 16.904 1508 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 9.87 % Allowed : 33.00 % Favored : 57.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.22), residues: 1445 helix: 2.39 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 480 TYR 0.018 0.001 TYR B 240 PHE 0.017 0.001 PHE B 568 TRP 0.017 0.001 TRP A 106 HIS 0.001 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 9733) covalent geometry : angle 0.60052 / 0.31 (13381) hydrogen bonds : bond 0.04202 / 3.02 ( 864) hydrogen bonds : angle 3.85030 / 2.87 ( 2562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 144 time to evaluate : 0.365 Fit side-chains REVERT: A 205 ASP cc_start: 0.8870 (t0) cc_final: 0.8570 (t70) REVERT: A 215 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 423 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.9052 (m-80) REVERT: A 471 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7018 (t0) REVERT: A 510 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8806 (mm-40) REVERT: A 520 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8228 (mmmt) REVERT: B 210 MET cc_start: 0.9469 (tpp) cc_final: 0.9253 (mmm) REVERT: B 481 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7910 (mp10) REVERT: B 497 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 518 GLU cc_start: 0.8456 (pp20) cc_final: 0.8039 (pp20) REVERT: B 548 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8994 (tp) REVERT: C 89 CYS cc_start: 0.8860 (m) cc_final: 0.8280 (t) REVERT: C 439 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9057 (mm-30) REVERT: C 475 ASP cc_start: 0.8733 (m-30) cc_final: 0.8428 (m-30) REVERT: C 507 CYS cc_start: 0.9023 (m) cc_final: 0.8444 (p) REVERT: C 510 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.9178 (tp40) outliers start: 70 outliers final: 49 residues processed: 190 average time/residue: 0.0623 time to fit residues: 18.6100 Evaluate side-chains 191 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.116370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091264 restraints weight = 29664.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093727 restraints weight = 15821.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095103 restraints weight = 10362.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096154 restraints weight = 8027.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096559 restraints weight = 6640.673| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9733 Z= 0.120 Angle : 0.581 12.169 13381 Z= 0.291 Chirality : 0.040 0.154 1712 Planarity : 0.003 0.027 1700 Dihedral : 3.625 16.300 1508 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 7.76 % Allowed : 34.84 % Favored : 57.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.22), residues: 1445 helix: 2.46 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 204 TYR 0.019 0.001 TYR B 240 PHE 0.014 0.001 PHE A 336 TRP 0.020 0.001 TRP A 106 HIS 0.001 0.000 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9733) covalent geometry : angle 0.58095 / 0.29 (13381) hydrogen bonds : bond 0.03773 / 2.74 ( 864) hydrogen bonds : angle 3.64952 / 2.71 ( 2562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 0.321 Fit side-chains REVERT: A 205 ASP cc_start: 0.8823 (t0) cc_final: 0.8505 (t0) REVERT: A 215 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8838 (tt) REVERT: A 471 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6846 (t0) REVERT: A 480 ARG cc_start: 0.4903 (mtt180) cc_final: 0.4351 (ttp-170) REVERT: A 510 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8718 (mm-40) REVERT: A 520 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8196 (mmmt) REVERT: A 557 TYR cc_start: 0.8724 (t80) cc_final: 0.8486 (t80) REVERT: B 153 ASP cc_start: 0.8104 (t0) cc_final: 0.7825 (m-30) REVERT: B 481 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: B 497 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8306 (t80) REVERT: B 518 GLU cc_start: 0.8430 (pp20) cc_final: 0.8021 (pp20) REVERT: B 548 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9067 (tp) REVERT: C 89 CYS cc_start: 0.8790 (m) cc_final: 0.8245 (t) REVERT: C 439 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8981 (mm-30) REVERT: C 475 ASP cc_start: 0.8665 (m-30) cc_final: 0.8371 (m-30) REVERT: C 507 CYS cc_start: 0.8923 (m) cc_final: 0.8400 (p) REVERT: C 510 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.8654 (tp40) outliers start: 55 outliers final: 41 residues processed: 188 average time/residue: 0.0705 time to fit residues: 20.3993 Evaluate side-chains 189 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 40.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.116243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091097 restraints weight = 30153.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093587 restraints weight = 16015.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095035 restraints weight = 10479.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096058 restraints weight = 7970.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096715 restraints weight = 6670.623| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9733 Z= 0.132 Angle : 0.594 11.944 13381 Z= 0.298 Chirality : 0.040 0.163 1712 Planarity : 0.003 0.028 1700 Dihedral : 3.621 16.508 1508 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 7.90 % Allowed : 35.12 % Favored : 56.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.22), residues: 1445 helix: 2.46 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.25 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 204 TYR 0.019 0.001 TYR B 240 PHE 0.017 0.001 PHE A 336 TRP 0.023 0.001 TRP A 106 HIS 0.001 0.000 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9733) covalent geometry : angle 0.59385 / 0.30 (13381) hydrogen bonds : bond 0.03762 / 2.72 ( 864) hydrogen bonds : angle 3.65238 / 2.71 ( 2562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 0.447 Fit side-chains REVERT: A 205 ASP cc_start: 0.8818 (t0) cc_final: 0.8512 (t70) REVERT: A 215 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 471 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6900 (t0) REVERT: A 480 ARG cc_start: 0.4910 (mtt180) cc_final: 0.4359 (ttp-170) REVERT: A 481 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8279 (mm-40) REVERT: A 520 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8200 (mmmt) REVERT: A 557 TYR cc_start: 0.8755 (t80) cc_final: 0.8512 (t80) REVERT: B 237 TYR cc_start: 0.9492 (t80) cc_final: 0.9281 (t80) REVERT: B 481 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: B 497 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8248 (t80) REVERT: B 518 GLU cc_start: 0.8451 (pp20) cc_final: 0.8044 (pp20) REVERT: B 548 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9113 (tt) REVERT: C 89 CYS cc_start: 0.8779 (m) cc_final: 0.8249 (t) REVERT: C 475 ASP cc_start: 0.8663 (m-30) cc_final: 0.8390 (m-30) REVERT: C 507 CYS cc_start: 0.8940 (m) cc_final: 0.8443 (p) REVERT: C 510 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8659 (tp40) outliers start: 56 outliers final: 43 residues processed: 186 average time/residue: 0.0667 time to fit residues: 19.2130 Evaluate side-chains 193 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.117412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092159 restraints weight = 29852.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094650 restraints weight = 15917.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096111 restraints weight = 10452.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097082 restraints weight = 7995.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.097567 restraints weight = 6680.926| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9733 Z= 0.121 Angle : 0.609 12.700 13381 Z= 0.298 Chirality : 0.040 0.156 1712 Planarity : 0.003 0.027 1700 Dihedral : 3.576 16.304 1508 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 7.33 % Allowed : 35.97 % Favored : 56.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.22), residues: 1445 helix: 2.48 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 204 TYR 0.019 0.001 TYR B 240 PHE 0.017 0.001 PHE A 336 TRP 0.024 0.001 TRP A 106 HIS 0.001 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9733) covalent geometry : angle 0.60892 / 0.30 (13381) hydrogen bonds : bond 0.03615 / 2.62 ( 864) hydrogen bonds : angle 3.59198 / 2.67 ( 2562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 0.250 Fit side-chains REVERT: A 205 ASP cc_start: 0.8781 (t0) cc_final: 0.8468 (t0) REVERT: A 215 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 471 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6911 (t0) REVERT: A 480 ARG cc_start: 0.4888 (mtt180) cc_final: 0.4353 (ttp-170) REVERT: A 481 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8262 (mm-40) REVERT: A 510 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8853 (mm-40) REVERT: A 520 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8203 (mmmt) REVERT: A 557 TYR cc_start: 0.8677 (t80) cc_final: 0.8405 (t80) REVERT: B 153 ASP cc_start: 0.7932 (m-30) cc_final: 0.7684 (m-30) REVERT: B 481 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: B 497 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 518 GLU cc_start: 0.8475 (pp20) cc_final: 0.8097 (pp20) REVERT: B 522 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 89 CYS cc_start: 0.8802 (m) cc_final: 0.8202 (t) REVERT: C 102 LEU cc_start: 0.9191 (tt) cc_final: 0.8896 (mt) REVERT: C 475 ASP cc_start: 0.8637 (m-30) cc_final: 0.8363 (m-30) REVERT: C 507 CYS cc_start: 0.8919 (m) cc_final: 0.8427 (p) REVERT: C 510 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8550 (tp40) outliers start: 52 outliers final: 43 residues processed: 190 average time/residue: 0.0731 time to fit residues: 21.2745 Evaluate side-chains 193 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 80 optimal weight: 0.0060 chunk 116 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 30.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** 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 = 0.3824 r_free = 0.3824 target = 0.116036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091527 restraints weight = 29635.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093957 restraints weight = 16227.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095484 restraints weight = 10674.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096255 restraints weight = 8068.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096653 restraints weight = 6849.680| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9733 Z= 0.119 Angle : 0.618 12.546 13381 Z= 0.304 Chirality : 0.041 0.187 1712 Planarity : 0.003 0.026 1700 Dihedral : 3.568 16.253 1508 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 6.06 % Allowed : 37.80 % Favored : 56.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.22), residues: 1445 helix: 2.46 (0.15), residues: 1147 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 204 TYR 0.020 0.001 TYR B 237 PHE 0.014 0.001 PHE B 217 TRP 0.023 0.001 TRP A 106 HIS 0.002 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9733) covalent geometry : angle 0.61785 / 0.30 (13381) hydrogen bonds : bond 0.03573 / 2.58 ( 864) hydrogen bonds : angle 3.56675 / 2.65 ( 2562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.351 Fit side-chains REVERT: A 205 ASP cc_start: 0.8761 (t0) cc_final: 0.8518 (t70) REVERT: A 215 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8850 (tt) REVERT: A 471 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6795 (t0) REVERT: A 480 ARG cc_start: 0.4864 (mtt180) cc_final: 0.4367 (ttp-170) REVERT: A 481 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8252 (mm-40) REVERT: A 510 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8833 (mm-40) REVERT: A 520 LYS cc_start: 0.8584 (mmtt) cc_final: 0.7991 (mmmt) REVERT: A 557 TYR cc_start: 0.8632 (t80) cc_final: 0.8339 (t80) REVERT: B 153 ASP cc_start: 0.8164 (m-30) cc_final: 0.7952 (m-30) REVERT: B 481 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: B 518 GLU cc_start: 0.8469 (pp20) cc_final: 0.8082 (pp20) REVERT: B 522 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7843 (tm-30) REVERT: C 85 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8292 (mmtt) REVERT: C 89 CYS cc_start: 0.8831 (m) cc_final: 0.8238 (t) REVERT: C 102 LEU cc_start: 0.9192 (tt) cc_final: 0.8898 (mt) REVERT: C 475 ASP cc_start: 0.8652 (m-30) cc_final: 0.8381 (m-30) REVERT: C 507 CYS cc_start: 0.8903 (m) cc_final: 0.8425 (p) REVERT: C 510 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8500 (tp40) outliers start: 43 outliers final: 36 residues processed: 177 average time/residue: 0.0730 time to fit residues: 19.8945 Evaluate side-chains 187 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 124 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** 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 = 0.3836 r_free = 0.3836 target = 0.118566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093703 restraints weight = 29819.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095959 restraints weight = 18062.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097844 restraints weight = 10813.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098045 restraints weight = 8197.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098199 restraints weight = 7796.376| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9733 Z= 0.113 Angle : 0.613 12.536 13381 Z= 0.300 Chirality : 0.041 0.165 1712 Planarity : 0.003 0.026 1700 Dihedral : 3.506 16.068 1508 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 6.35 % Allowed : 37.38 % Favored : 56.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.22), residues: 1445 helix: 2.50 (0.15), residues: 1147 sheet: None (None), residues: 0 loop : -0.19 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 204 TYR 0.020 0.001 TYR B 240 PHE 0.014 0.001 PHE B 217 TRP 0.064 0.002 TRP A 419 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9733) covalent geometry : angle 0.61313 / 0.30 (13381) hydrogen bonds : bond 0.03374 / 2.45 ( 864) hydrogen bonds : angle 3.52118 / 2.62 ( 2562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.04 seconds wall clock time: 27 minutes 34.48 seconds (1654.48 seconds total)