Starting phenix.real_space_refine on Tue Feb 3 23:57:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rpt_54171/02_2026/9rpt_54171.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rpt_54171/02_2026/9rpt_54171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rpt_54171/02_2026/9rpt_54171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rpt_54171/02_2026/9rpt_54171.map" model { file = "/net/cci-nas-00/data/ceres_data/9rpt_54171/02_2026/9rpt_54171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rpt_54171/02_2026/9rpt_54171.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 32 5.16 5 C 4884 2.51 5 N 1353 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7761 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4665 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 2 Chain: "B" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 1 Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1938 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 13, 'TRANS': 240} Chain breaks: 2 Time building chain proxies: 1.70, per 1000 atoms: 0.22 Number of scatterers: 7761 At special positions: 0 Unit cell: (76.96, 103.6, 113.22, 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 32 16.00 O 1492 8.00 N 1353 7.00 C 4884 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: 0.66 Conformation dependent library (CDL) restraints added in 325.5 milliseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 9.2% alpha, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.616A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.759A pdb=" N ARG A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.740A pdb=" N PHE A 541 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 668 Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.878A pdb=" N ASN B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 207 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 242 through 244 current: chain 'A' and resid 255 through 264 removed outlier: 3.523A pdb=" N ASN A 269 " --> pdb=" O MET A 264 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 325 through 334 current: chain 'A' and resid 354 through 365 removed outlier: 4.341A pdb=" N ALA A 355 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LYS A 375 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU A 391 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE A 377 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N SER A 389 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA A 390 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 418 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 427 " --> pdb=" O PHE A 417 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 426 through 432 current: chain 'A' and resid 445 through 461 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 477 through 491 current: chain 'A' and resid 505 through 517 removed outlier: 7.639A pdb=" N ASN A 556 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR A 584 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 558 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE A 582 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 560 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 580 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 562 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A 578 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 564 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 576 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 566 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ARG A 574 " --> pdb=" O TRP A 614 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP A 614 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN A 576 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 612 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 578 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A 610 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY A 580 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP A 608 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 582 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 637 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP A 629 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL A 635 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 651 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP A 706 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN A 712 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 13.072A pdb=" N LYS A 711 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 13.044A pdb=" N GLY A 738 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ALA A 713 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 736 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 747 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.776A pdb=" N MET B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU B 75 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 37 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU B 77 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 39 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N LYS B 79 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN B 105 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 80 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 103 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE B 82 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 101 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 84 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLN B 99 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR B 86 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLU B 97 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N SER B 88 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR B 95 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 26 through 34 removed outlier: 6.911A pdb=" N ILE C 111 " --> pdb=" O CYS C 28 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER C 30 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY C 109 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN C 32 " --> pdb=" O TRP C 107 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP C 107 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA C 108 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 44 removed outlier: 6.816A pdb=" N GLY C 89 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG C 84 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 91 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 82 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG C 93 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 233 through 234 removed outlier: 4.180A pdb=" N LYS C 233 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N CYS C 144 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN C 207 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 146 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 167 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP C 168 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N SER C 253 " --> pdb=" O TRP C 168 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU C 315 " --> pdb=" O GLN C 256 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 239 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 155 through 157 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 155 through 157 current: chain 'C' and resid 181 through 186 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 181 through 186 current: chain 'C' and resid 270 through 281 removed outlier: 3.700A pdb=" N TYR C 296 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 294 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET C 275 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 292 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY C 277 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C 290 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG C 279 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA C 288 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA C 281 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG C 286 " --> pdb=" O ALA C 281 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 804 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: 1.37 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2593 1.34 - 1.46: 1719 1.46 - 1.58: 3567 1.58 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 7938 Sorted by residual: bond pdb=" C LEU A 668 " pdb=" N PRO A 669 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.24e-01 bond pdb=" N GLY A 718 " pdb=" CA GLY A 718 " ideal model delta sigma weight residual 1.448 1.455 -0.007 1.04e-02 9.25e+03 4.43e-01 bond pdb=" CA TYR A 240 " pdb=" CB TYR A 240 " ideal model delta sigma weight residual 1.517 1.532 -0.016 2.41e-02 1.72e+03 4.17e-01 bond pdb=" CB PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.13e-01 bond pdb=" N VAL C 310 " pdb=" CA VAL C 310 " ideal model delta sigma weight residual 1.468 1.462 0.007 1.05e-02 9.07e+03 4.10e-01 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 10396 1.04 - 2.08: 305 2.08 - 3.12: 61 3.12 - 4.16: 17 4.16 - 5.20: 5 Bond angle restraints: 10784 Sorted by residual: angle pdb=" C TYR A 240 " pdb=" CA TYR A 240 " pdb=" CB TYR A 240 " ideal model delta sigma weight residual 115.89 110.69 5.20 1.32e+00 5.74e-01 1.55e+01 angle pdb=" N ARG B 56 " pdb=" CA ARG B 56 " pdb=" C ARG B 56 " ideal model delta sigma weight residual 113.18 108.94 4.24 1.33e+00 5.65e-01 1.02e+01 angle pdb=" C ASN C 290 " pdb=" N ARG C 291 " pdb=" CA ARG C 291 " ideal model delta sigma weight residual 121.31 124.91 -3.60 1.49e+00 4.50e-01 5.84e+00 angle pdb=" CA LEU B 55 " pdb=" C LEU B 55 " pdb=" N ARG B 56 " ideal model delta sigma weight residual 117.51 114.33 3.18 1.32e+00 5.74e-01 5.82e+00 angle pdb=" N LEU B 57 " pdb=" CA LEU B 57 " pdb=" C LEU B 57 " ideal model delta sigma weight residual 113.01 110.40 2.61 1.20e+00 6.94e-01 4.71e+00 ... (remaining 10779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4431 17.43 - 34.86: 204 34.86 - 52.29: 51 52.29 - 69.72: 17 69.72 - 87.15: 6 Dihedral angle restraints: 4709 sinusoidal: 1878 harmonic: 2831 Sorted by residual: dihedral pdb=" CA TYR A 678 " pdb=" C TYR A 678 " pdb=" N LYS A 679 " pdb=" CA LYS A 679 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB ARG B 157 " pdb=" CG ARG B 157 " pdb=" CD ARG B 157 " pdb=" NE ARG B 157 " ideal model delta sinusoidal sigma weight residual -180.00 -120.09 -59.91 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 163 " pdb=" CB ARG B 163 " pdb=" CG ARG B 163 " pdb=" CD ARG B 163 " ideal model delta sinusoidal sigma weight residual 60.00 118.56 -58.56 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 643 0.028 - 0.056: 310 0.056 - 0.084: 90 0.084 - 0.112: 70 0.112 - 0.139: 39 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE A 525 " pdb=" N ILE A 525 " pdb=" C ILE A 525 " pdb=" CB ILE A 525 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL A 652 " pdb=" N VAL A 652 " pdb=" C VAL A 652 " pdb=" CB VAL A 652 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1149 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 391 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 392 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 252 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 253 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 159 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO B 160 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.020 5.00e-02 4.00e+02 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 4347 3.04 - 3.51: 6872 3.51 - 3.97: 12251 3.97 - 4.44: 14704 4.44 - 4.90: 25080 Nonbonded interactions: 63254 Sorted by model distance: nonbonded pdb=" N VAL A 365 " pdb=" O VAL A 365 " model vdw 2.577 2.496 nonbonded pdb=" N ASP A 536 " pdb=" O ASP A 536 " model vdw 2.598 2.496 nonbonded pdb=" O GLN C 69 " pdb=" OG1 THR C 70 " model vdw 2.599 3.040 nonbonded pdb=" N ALA A 252 " pdb=" O ALA A 252 " model vdw 2.623 2.496 nonbonded pdb=" N ASN A 442 " pdb=" O ASN A 442 " model vdw 2.623 2.496 ... (remaining 63249 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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 0.032 7938 Z= 0.115 Angle : 0.471 5.197 10784 Z= 0.258 Chirality : 0.045 0.139 1152 Planarity : 0.004 0.040 1419 Dihedral : 11.860 87.152 2903 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.95 % Allowed : 7.15 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.88 (0.26), residues: 953 helix: -2.26 (0.48), residues: 76 sheet: 0.06 (0.24), residues: 468 loop : -0.91 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.016 0.001 TYR A 678 PHE 0.007 0.001 PHE A 241 TRP 0.005 0.001 TRP A 465 HIS 0.002 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7938) covalent geometry : angle 0.47070 (10784) hydrogen bonds : bond 0.21994 ( 284) hydrogen bonds : angle 9.65172 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.318 Fit side-chains REVERT: A 784 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7706 (mp) REVERT: C 69 GLN cc_start: 0.7585 (tt0) cc_final: 0.7208 (tt0) REVERT: C 233 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7446 (mppt) outliers start: 8 outliers final: 0 residues processed: 102 average time/residue: 0.6384 time to fit residues: 68.5545 Evaluate side-chains 75 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 784 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS A 302 HIS A 557 GLN A 677 GLN B 53 ASN B 129 ASN B 131 GLN C 252 ASN C 300 GLN C 302 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.068421 restraints weight = 13190.542| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.46 r_work: 0.2764 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 7938 Z= 0.276 Angle : 0.582 7.644 10784 Z= 0.314 Chirality : 0.048 0.152 1152 Planarity : 0.005 0.043 1419 Dihedral : 4.821 50.213 1092 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.98 % Allowed : 10.01 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.61 (0.26), residues: 953 helix: -0.13 (0.59), residues: 83 sheet: 0.07 (0.24), residues: 463 loop : -0.93 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 469 TYR 0.019 0.002 TYR A 678 PHE 0.010 0.002 PHE A 241 TRP 0.007 0.001 TRP A 465 HIS 0.004 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 7938) covalent geometry : angle 0.58195 (10784) hydrogen bonds : bond 0.04902 ( 284) hydrogen bonds : angle 6.48952 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.241 Fit side-chains REVERT: A 646 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7229 (ttp-170) REVERT: B 145 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8284 (ttpp) REVERT: C 233 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6871 (mtmt) outliers start: 25 outliers final: 10 residues processed: 92 average time/residue: 0.5185 time to fit residues: 50.8207 Evaluate side-chains 79 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.070329 restraints weight = 12871.126| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.44 r_work: 0.2803 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7938 Z= 0.135 Angle : 0.491 5.893 10784 Z= 0.261 Chirality : 0.045 0.140 1152 Planarity : 0.004 0.041 1419 Dihedral : 4.303 15.862 1090 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.38 % Allowed : 11.32 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.27 (0.27), residues: 953 helix: 0.56 (0.60), residues: 82 sheet: 0.29 (0.24), residues: 461 loop : -0.80 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 469 TYR 0.013 0.001 TYR A 678 PHE 0.007 0.001 PHE A 327 TRP 0.005 0.001 TRP A 311 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7938) covalent geometry : angle 0.49056 (10784) hydrogen bonds : bond 0.03718 ( 284) hydrogen bonds : angle 5.88710 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.314 Fit side-chains REVERT: A 366 GLN cc_start: 0.8713 (tt0) cc_final: 0.8513 (pm20) REVERT: A 646 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: C 233 LYS cc_start: 0.7554 (mtpt) cc_final: 0.6536 (mptt) outliers start: 20 outliers final: 7 residues processed: 86 average time/residue: 0.5837 time to fit residues: 53.0659 Evaluate side-chains 77 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.087400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.068857 restraints weight = 13188.359| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.49 r_work: 0.2777 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7938 Z= 0.201 Angle : 0.525 5.861 10784 Z= 0.279 Chirality : 0.046 0.146 1152 Planarity : 0.004 0.041 1419 Dihedral : 4.366 16.786 1090 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.15 % Allowed : 12.99 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 953 helix: 0.77 (0.60), residues: 82 sheet: 0.35 (0.24), residues: 458 loop : -0.84 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 469 TYR 0.015 0.001 TYR A 678 PHE 0.008 0.001 PHE A 406 TRP 0.007 0.001 TRP A 739 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 7938) covalent geometry : angle 0.52470 (10784) hydrogen bonds : bond 0.03833 ( 284) hydrogen bonds : angle 5.78878 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.299 Fit side-chains REVERT: A 592 ASP cc_start: 0.8294 (t0) cc_final: 0.8084 (t0) REVERT: A 646 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7283 (ttp-170) REVERT: C 233 LYS cc_start: 0.7565 (mtpt) cc_final: 0.6560 (mptt) outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.5875 time to fit residues: 51.7578 Evaluate side-chains 76 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.069926 restraints weight = 13042.384| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.45 r_work: 0.2798 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7938 Z= 0.138 Angle : 0.485 6.134 10784 Z= 0.258 Chirality : 0.045 0.139 1152 Planarity : 0.004 0.041 1419 Dihedral : 4.226 15.826 1090 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.15 % Allowed : 13.35 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.05 (0.27), residues: 953 helix: 1.05 (0.59), residues: 82 sheet: 0.39 (0.24), residues: 469 loop : -0.70 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 469 TYR 0.012 0.001 TYR A 678 PHE 0.007 0.001 PHE A 754 TRP 0.006 0.001 TRP A 739 HIS 0.005 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7938) covalent geometry : angle 0.48522 (10784) hydrogen bonds : bond 0.03366 ( 284) hydrogen bonds : angle 5.53986 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.388 Fit side-chains REVERT: A 366 GLN cc_start: 0.8883 (tt0) cc_final: 0.8502 (pm20) REVERT: A 646 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7304 (ttp-170) REVERT: B 115 ILE cc_start: 0.9104 (mm) cc_final: 0.8761 (tp) REVERT: C 233 LYS cc_start: 0.7613 (mtpt) cc_final: 0.6613 (mptt) outliers start: 18 outliers final: 9 residues processed: 84 average time/residue: 0.5884 time to fit residues: 52.5499 Evaluate side-chains 77 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.087439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.069026 restraints weight = 13065.923| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.44 r_work: 0.2779 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7938 Z= 0.191 Angle : 0.521 6.950 10784 Z= 0.276 Chirality : 0.046 0.162 1152 Planarity : 0.004 0.045 1419 Dihedral : 4.303 16.298 1090 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.74 % Allowed : 13.47 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.11 (0.27), residues: 953 helix: 1.10 (0.59), residues: 82 sheet: 0.35 (0.24), residues: 464 loop : -0.75 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 469 TYR 0.014 0.001 TYR A 678 PHE 0.008 0.001 PHE A 406 TRP 0.007 0.001 TRP A 739 HIS 0.005 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 7938) covalent geometry : angle 0.52140 (10784) hydrogen bonds : bond 0.03601 ( 284) hydrogen bonds : angle 5.58243 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.314 Fit side-chains REVERT: C 233 LYS cc_start: 0.7637 (mtpt) cc_final: 0.6620 (mptt) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.5471 time to fit residues: 50.1508 Evaluate side-chains 83 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 0.0050 chunk 56 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 0.0270 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 54 optimal weight: 0.2980 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN B 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.072664 restraints weight = 12877.557| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.50 r_work: 0.2855 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7938 Z= 0.081 Angle : 0.461 7.083 10784 Z= 0.242 Chirality : 0.044 0.136 1152 Planarity : 0.004 0.046 1419 Dihedral : 3.970 15.281 1090 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 14.78 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.16 (0.27), residues: 953 helix: 1.36 (0.60), residues: 82 sheet: 0.49 (0.24), residues: 467 loop : -0.53 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 469 TYR 0.010 0.001 TYR A 705 PHE 0.007 0.001 PHE A 754 TRP 0.005 0.000 TRP A 739 HIS 0.005 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 7938) covalent geometry : angle 0.46050 (10784) hydrogen bonds : bond 0.02690 ( 284) hydrogen bonds : angle 5.11352 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8896 (tt0) cc_final: 0.8492 (pm20) REVERT: B 75 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7924 (tp) REVERT: C 62 GLU cc_start: 0.8294 (tp30) cc_final: 0.7242 (tp30) REVERT: C 69 GLN cc_start: 0.7742 (tt0) cc_final: 0.7416 (mt0) REVERT: C 233 LYS cc_start: 0.7496 (mtpt) cc_final: 0.6496 (mptt) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.5685 time to fit residues: 54.3743 Evaluate side-chains 88 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.0030 chunk 38 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.071266 restraints weight = 13026.670| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.43 r_work: 0.2820 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7938 Z= 0.121 Angle : 0.483 8.079 10784 Z= 0.253 Chirality : 0.045 0.134 1152 Planarity : 0.004 0.053 1419 Dihedral : 4.014 15.445 1090 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.79 % Allowed : 15.26 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.19 (0.27), residues: 953 helix: 1.40 (0.60), residues: 82 sheet: 0.52 (0.24), residues: 469 loop : -0.54 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 469 TYR 0.010 0.001 TYR A 678 PHE 0.007 0.001 PHE A 406 TRP 0.006 0.001 TRP A 739 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7938) covalent geometry : angle 0.48273 (10784) hydrogen bonds : bond 0.02924 ( 284) hydrogen bonds : angle 5.15424 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.294 Fit side-chains REVERT: A 366 GLN cc_start: 0.8884 (tt0) cc_final: 0.8492 (pm20) REVERT: B 75 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7971 (tp) REVERT: C 69 GLN cc_start: 0.7641 (tt0) cc_final: 0.7297 (mt0) REVERT: C 233 LYS cc_start: 0.7562 (mtpt) cc_final: 0.6567 (mptt) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.5356 time to fit residues: 49.0377 Evaluate side-chains 87 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.070592 restraints weight = 12912.439| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.43 r_work: 0.2810 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7938 Z= 0.140 Angle : 0.499 9.261 10784 Z= 0.261 Chirality : 0.045 0.135 1152 Planarity : 0.004 0.051 1419 Dihedral : 4.102 15.286 1090 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.91 % Allowed : 15.61 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.16 (0.27), residues: 953 helix: 1.39 (0.60), residues: 82 sheet: 0.50 (0.24), residues: 469 loop : -0.57 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 469 TYR 0.012 0.001 TYR A 678 PHE 0.008 0.001 PHE A 406 TRP 0.006 0.001 TRP A 739 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7938) covalent geometry : angle 0.49880 (10784) hydrogen bonds : bond 0.03086 ( 284) hydrogen bonds : angle 5.22837 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.311 Fit side-chains REVERT: A 366 GLN cc_start: 0.8885 (tt0) cc_final: 0.8488 (pm20) REVERT: B 75 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 69 GLN cc_start: 0.7773 (tt0) cc_final: 0.7372 (mt0) REVERT: C 233 LYS cc_start: 0.7652 (mtpt) cc_final: 0.6633 (mptt) outliers start: 16 outliers final: 12 residues processed: 87 average time/residue: 0.4890 time to fit residues: 45.2574 Evaluate side-chains 85 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN B 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.087299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068871 restraints weight = 12981.133| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.43 r_work: 0.2781 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7938 Z= 0.216 Angle : 0.550 9.913 10784 Z= 0.289 Chirality : 0.047 0.136 1152 Planarity : 0.004 0.057 1419 Dihedral : 4.307 16.252 1090 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.91 % Allowed : 15.49 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 953 helix: 1.30 (0.60), residues: 82 sheet: 0.40 (0.24), residues: 484 loop : -0.65 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 469 TYR 0.014 0.001 TYR A 678 PHE 0.010 0.001 PHE A 406 TRP 0.007 0.001 TRP A 739 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 7938) covalent geometry : angle 0.55011 (10784) hydrogen bonds : bond 0.03558 ( 284) hydrogen bonds : angle 5.49449 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.277 Fit side-chains REVERT: B 75 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 233 LYS cc_start: 0.7661 (mtpt) cc_final: 0.6619 (mptt) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.4888 time to fit residues: 43.6336 Evaluate side-chains 84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.069298 restraints weight = 13070.483| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.45 r_work: 0.2789 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7938 Z= 0.177 Angle : 0.532 10.443 10784 Z= 0.279 Chirality : 0.046 0.137 1152 Planarity : 0.004 0.054 1419 Dihedral : 4.278 16.017 1090 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.03 % Allowed : 15.49 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.00 (0.27), residues: 953 helix: 1.31 (0.60), residues: 82 sheet: 0.37 (0.24), residues: 484 loop : -0.67 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 469 TYR 0.013 0.001 TYR A 678 PHE 0.009 0.001 PHE A 754 TRP 0.006 0.001 TRP A 739 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7938) covalent geometry : angle 0.53244 (10784) hydrogen bonds : bond 0.03400 ( 284) hydrogen bonds : angle 5.44754 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.47 seconds wall clock time: 44 minutes 11.28 seconds (2651.28 seconds total)