Starting phenix.real_space_refine on Wed Mar 12 06:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9o_36112/03_2025/8j9o_36112_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9o_36112/03_2025/8j9o_36112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9o_36112/03_2025/8j9o_36112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9o_36112/03_2025/8j9o_36112.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9o_36112/03_2025/8j9o_36112_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9o_36112/03_2025/8j9o_36112_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 33 5.16 5 C 4758 2.51 5 N 1240 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7441 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3336 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 4 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1633 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 891 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1581 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.50, per 1000 atoms: 0.60 Number of scatterers: 7441 At special positions: 0 Unit cell: (69.056, 99.008, 153.92, 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 33 16.00 O 1410 8.00 N 1240 7.00 C 4758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.03 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 34.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 312 through 344 removed outlier: 3.508A pdb=" N TRP A 326 " --> pdb=" O TRP A 322 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 removed outlier: 3.748A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 431 removed outlier: 4.347A pdb=" N PHE A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.703A pdb=" N GLU A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.710A pdb=" N ILE A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 514 Processing helix chain 'A' and resid 1002 through 1025 removed outlier: 3.873A pdb=" N THR A1014 " --> pdb=" O ASP A1010 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1048 removed outlier: 3.569A pdb=" N VAL A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1041 " --> pdb=" O LYS A1037 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1068 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.549A pdb=" N LEU A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 removed outlier: 3.629A pdb=" N ALA A1094 " --> pdb=" O LYS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 removed outlier: 3.757A pdb=" N THR A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'A' and resid 531 through 556 Proline residue: A 547 - end of helix removed outlier: 4.009A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 574 removed outlier: 4.178A pdb=" N ARG A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 571 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.621A pdb=" N PHE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 608 " --> pdb=" O MET A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 622 removed outlier: 4.092A pdb=" N GLY A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 622 " --> pdb=" O GLY A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 removed outlier: 3.524A pdb=" N PHE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.700A pdb=" N LYS B 68 " --> pdb=" O ASP B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.917A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.678A pdb=" N LYS B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.103A pdb=" N VAL D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 382 removed outlier: 4.184A pdb=" N THR A 392 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.628A pdb=" N ASP A 469 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.531A pdb=" N GLN B 6 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 10 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.508A pdb=" N ALA B 100 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR B 53 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 53 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER B 62 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 55 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 134 through 138 removed outlier: 4.304A pdb=" N GLY B 153 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR B 190 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.559A pdb=" N ASN B 211 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.590A pdb=" N CYS C 22 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.956A pdb=" N ARG C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 40 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 99 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 39 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.582A pdb=" N VAL D 20 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.532A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 91 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.532A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.508A pdb=" N SER D 116 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 139 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 134 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 177 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.601A pdb=" N ALA D 195 " --> pdb=" O LYS D 151 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 945 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: 2.18 Time building geometry restraints manager: 1.98 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: 2353 1.34 - 1.46: 1682 1.46 - 1.58: 3537 1.58 - 1.70: 0 1.70 - 1.81: 45 Bond restraints: 7617 Sorted by residual: bond pdb=" CA VAL A 305 " pdb=" CB VAL A 305 " ideal model delta sigma weight residual 1.533 1.550 -0.017 1.20e-02 6.94e+03 2.02e+00 bond pdb=" CB PRO A 547 " pdb=" CG PRO A 547 " ideal model delta sigma weight residual 1.492 1.424 0.068 5.00e-02 4.00e+02 1.86e+00 bond pdb=" C SER D 8 " pdb=" N PRO D 9 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" N MET A 309 " pdb=" CA MET A 309 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" CB ASN D 160 " pdb=" CG ASN D 160 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 7612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 10164 2.15 - 4.30: 177 4.30 - 6.45: 33 6.45 - 8.60: 8 8.60 - 10.74: 5 Bond angle restraints: 10387 Sorted by residual: angle pdb=" C LEU A 308 " pdb=" N MET A 309 " pdb=" CA MET A 309 " ideal model delta sigma weight residual 121.54 132.25 -10.71 1.91e+00 2.74e-01 3.15e+01 angle pdb=" N VAL A 484 " pdb=" CA VAL A 484 " pdb=" C VAL A 484 " ideal model delta sigma weight residual 113.42 108.34 5.08 1.17e+00 7.31e-01 1.89e+01 angle pdb=" CA MET A 309 " pdb=" CB MET A 309 " pdb=" CG MET A 309 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C LYS C 87 " pdb=" CA LYS C 87 " pdb=" CB LYS C 87 " ideal model delta sigma weight residual 110.02 115.24 -5.22 1.50e+00 4.44e-01 1.21e+01 angle pdb=" CA LYS C 87 " pdb=" CB LYS C 87 " pdb=" CG LYS C 87 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.47e+00 ... (remaining 10382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4075 17.74 - 35.49: 310 35.49 - 53.23: 46 53.23 - 70.98: 8 70.98 - 88.72: 7 Dihedral angle restraints: 4446 sinusoidal: 1553 harmonic: 2893 Sorted by residual: dihedral pdb=" CA TRP B 105 " pdb=" C TRP B 105 " pdb=" N PRO B 106 " pdb=" CA PRO B 106 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CB CYS A 402 " pdb=" SG CYS A 402 " pdb=" SG CYS A 477 " pdb=" CB CYS A 477 " ideal model delta sinusoidal sigma weight residual -86.00 -131.87 45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 574 " pdb=" SG CYS A 574 " pdb=" SG CYS A 581 " pdb=" CB CYS A 581 " ideal model delta sinusoidal sigma weight residual 93.00 132.73 -39.73 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 766 0.037 - 0.074: 305 0.074 - 0.110: 87 0.110 - 0.147: 27 0.147 - 0.184: 2 Chirality restraints: 1187 Sorted by residual: chirality pdb=" CA VAL A 454 " pdb=" N VAL A 454 " pdb=" C VAL A 454 " pdb=" CB VAL A 454 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB VAL A 454 " pdb=" CA VAL A 454 " pdb=" CG1 VAL A 454 " pdb=" CG2 VAL A 454 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE C 29 " pdb=" CA ILE C 29 " pdb=" CG1 ILE C 29 " pdb=" CG2 ILE C 29 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1184 not shown) Planarity restraints: 1315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 546 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 547 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO A 283 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 350 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO A 351 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.038 5.00e-02 4.00e+02 ... (remaining 1312 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 455 2.73 - 3.28: 7345 3.28 - 3.82: 12150 3.82 - 4.36: 14034 4.36 - 4.90: 24298 Nonbonded interactions: 58282 Sorted by model distance: nonbonded pdb=" OG1 THR A1014 " pdb=" OD1 ASN A1018 " model vdw 2.192 3.040 nonbonded pdb=" OG SER C 100 " pdb=" OG SER C 107 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 167 " pdb=" OD1 ASN B 211 " model vdw 2.222 3.040 nonbonded pdb=" NE2 GLN D 91 " pdb=" O LEU D 97 " model vdw 2.232 3.120 nonbonded pdb=" OG SER D 66 " pdb=" OG1 THR D 73 " model vdw 2.261 3.040 ... (remaining 58277 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: 1.040 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.530 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 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 0.068 7617 Z= 0.207 Angle : 0.748 10.744 10387 Z= 0.385 Chirality : 0.044 0.184 1187 Planarity : 0.006 0.101 1315 Dihedral : 13.166 88.719 2566 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 983 helix: -0.73 (0.27), residues: 309 sheet: -0.47 (0.36), residues: 204 loop : -1.69 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.003 0.001 HIS B 178 PHE 0.014 0.001 PHE A 561 TYR 0.016 0.001 TYR D 92 ARG 0.002 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ILE cc_start: 0.7724 (mt) cc_final: 0.7505 (mt) REVERT: A 506 LEU cc_start: 0.7887 (mm) cc_final: 0.7624 (mp) REVERT: A 1004 GLN cc_start: 0.7471 (mp10) cc_final: 0.6838 (mp10) REVERT: A 1018 ASN cc_start: 0.6637 (m110) cc_final: 0.6197 (m110) REVERT: A 1115 ARG cc_start: 0.6903 (ptm160) cc_final: 0.6638 (ptm160) REVERT: B 71 PHE cc_start: 0.7277 (m-80) cc_final: 0.6950 (m-80) REVERT: B 80 ASN cc_start: 0.7262 (t0) cc_final: 0.6832 (t0) REVERT: C 46 GLU cc_start: 0.6171 (mp0) cc_final: 0.5585 (mp0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1903 time to fit residues: 57.0941 Evaluate side-chains 202 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 89 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN D 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127982 restraints weight = 12562.312| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.81 r_work: 0.3519 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 7617 Z= 0.358 Angle : 0.674 9.769 10387 Z= 0.350 Chirality : 0.043 0.154 1187 Planarity : 0.006 0.076 1315 Dihedral : 4.609 30.457 1071 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.78 % Allowed : 10.85 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 983 helix: -0.23 (0.28), residues: 326 sheet: -0.82 (0.34), residues: 236 loop : -1.70 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 322 HIS 0.002 0.001 HIS B 214 PHE 0.018 0.002 PHE A1066 TYR 0.019 0.002 TYR D 92 ARG 0.005 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 PHE cc_start: 0.6833 (t80) cc_final: 0.6618 (t80) REVERT: A 294 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7414 (tmtt) REVERT: A 320 ARG cc_start: 0.6332 (tpp80) cc_final: 0.5467 (tpp80) REVERT: A 506 LEU cc_start: 0.8072 (mm) cc_final: 0.7755 (mp) REVERT: A 1004 GLN cc_start: 0.7993 (mp10) cc_final: 0.7458 (mp10) REVERT: A 1012 TRP cc_start: 0.8783 (t-100) cc_final: 0.8456 (t-100) REVERT: A 1018 ASN cc_start: 0.7604 (m110) cc_final: 0.7251 (m110) REVERT: A 1033 ASP cc_start: 0.7894 (t0) cc_final: 0.7547 (t0) REVERT: A 543 LEU cc_start: 0.7996 (tp) cc_final: 0.7726 (tt) REVERT: B 80 ASN cc_start: 0.7958 (t0) cc_final: 0.7610 (t0) REVERT: B 157 LYS cc_start: 0.7745 (tttt) cc_final: 0.7424 (tttt) REVERT: C 32 TYR cc_start: 0.7470 (m-80) cc_final: 0.7107 (m-80) REVERT: C 46 GLU cc_start: 0.6833 (mp0) cc_final: 0.6110 (mp0) outliers start: 21 outliers final: 14 residues processed: 226 average time/residue: 0.2011 time to fit residues: 60.9944 Evaluate side-chains 232 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 67 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN B 169 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.158145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130803 restraints weight = 12800.382| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.89 r_work: 0.3560 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7617 Z= 0.168 Angle : 0.598 9.723 10387 Z= 0.301 Chirality : 0.041 0.134 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.305 27.557 1071 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.31 % Allowed : 14.81 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 983 helix: 0.30 (0.29), residues: 325 sheet: -0.27 (0.37), residues: 203 loop : -1.75 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 420 HIS 0.001 0.000 HIS B 38 PHE 0.012 0.001 PHE A1066 TYR 0.018 0.001 TYR A1110 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7398 (tmtt) REVERT: A 309 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6828 (mtm) REVERT: A 320 ARG cc_start: 0.6398 (tpp80) cc_final: 0.5548 (tpp80) REVERT: A 443 ASN cc_start: 0.6959 (m-40) cc_final: 0.6495 (t0) REVERT: A 506 LEU cc_start: 0.7974 (mm) cc_final: 0.7683 (mp) REVERT: A 1004 GLN cc_start: 0.7976 (mp10) cc_final: 0.7410 (mp10) REVERT: A 1018 ASN cc_start: 0.7446 (m110) cc_final: 0.7112 (m110) REVERT: A 1033 ASP cc_start: 0.7870 (t0) cc_final: 0.7520 (t0) REVERT: A 1078 ASP cc_start: 0.7334 (m-30) cc_final: 0.7114 (m-30) REVERT: A 1079 ASP cc_start: 0.7161 (m-30) cc_final: 0.6944 (m-30) REVERT: A 543 LEU cc_start: 0.7968 (tp) cc_final: 0.7695 (tt) REVERT: B 50 TRP cc_start: 0.8568 (t60) cc_final: 0.8081 (t60) REVERT: B 80 ASN cc_start: 0.7900 (t0) cc_final: 0.7538 (t0) REVERT: B 157 LYS cc_start: 0.7738 (tttt) cc_final: 0.7421 (tttt) REVERT: C 32 TYR cc_start: 0.7393 (m-80) cc_final: 0.7050 (m-80) REVERT: C 46 GLU cc_start: 0.6734 (mp0) cc_final: 0.6013 (mp0) outliers start: 25 outliers final: 17 residues processed: 234 average time/residue: 0.1919 time to fit residues: 60.0143 Evaluate side-chains 238 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1098 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN B 169 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.158276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131290 restraints weight = 12684.613| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.88 r_work: 0.3559 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7617 Z= 0.177 Angle : 0.597 9.724 10387 Z= 0.297 Chirality : 0.041 0.137 1187 Planarity : 0.005 0.062 1315 Dihedral : 4.157 26.418 1071 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.23 % Allowed : 17.99 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.27), residues: 983 helix: 0.57 (0.29), residues: 326 sheet: -0.59 (0.35), residues: 221 loop : -1.63 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.010 0.001 PHE A1066 TYR 0.021 0.001 TYR C 104 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7447 (tmtt) REVERT: A 309 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6923 (mtm) REVERT: A 320 ARG cc_start: 0.6379 (tpp80) cc_final: 0.5495 (tpp80) REVERT: A 382 ASN cc_start: 0.7764 (t0) cc_final: 0.7557 (t0) REVERT: A 414 MET cc_start: 0.7535 (mmp) cc_final: 0.7155 (mmm) REVERT: A 506 LEU cc_start: 0.7969 (mm) cc_final: 0.7647 (mp) REVERT: A 1004 GLN cc_start: 0.7974 (mp10) cc_final: 0.7445 (mp10) REVERT: A 1018 ASN cc_start: 0.7448 (m110) cc_final: 0.7160 (m110) REVERT: A 1033 ASP cc_start: 0.7872 (t0) cc_final: 0.7510 (t0) REVERT: A 1046 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8109 (mt0) REVERT: A 1078 ASP cc_start: 0.7337 (m-30) cc_final: 0.7137 (m-30) REVERT: A 1079 ASP cc_start: 0.7231 (m-30) cc_final: 0.6978 (m-30) REVERT: A 543 LEU cc_start: 0.7964 (tp) cc_final: 0.7689 (tt) REVERT: A 565 TRP cc_start: 0.6853 (m-10) cc_final: 0.6600 (m-10) REVERT: B 50 TRP cc_start: 0.8570 (t60) cc_final: 0.8301 (t60) REVERT: B 80 ASN cc_start: 0.7934 (t0) cc_final: 0.7612 (t0) REVERT: B 157 LYS cc_start: 0.7742 (tttt) cc_final: 0.7440 (tttt) REVERT: C 32 TYR cc_start: 0.7405 (m-80) cc_final: 0.7068 (m-80) REVERT: C 46 GLU cc_start: 0.6728 (mp0) cc_final: 0.5971 (mp0) outliers start: 32 outliers final: 24 residues processed: 238 average time/residue: 0.2015 time to fit residues: 63.8964 Evaluate side-chains 243 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.159786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133451 restraints weight = 12537.859| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.82 r_work: 0.3555 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7617 Z= 0.203 Angle : 0.600 9.907 10387 Z= 0.300 Chirality : 0.041 0.140 1187 Planarity : 0.005 0.062 1315 Dihedral : 4.222 26.381 1071 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.89 % Allowed : 18.92 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.27), residues: 983 helix: 0.66 (0.29), residues: 326 sheet: -0.21 (0.37), residues: 196 loop : -1.65 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.009 0.001 PHE A1066 TYR 0.021 0.001 TYR A1110 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7776 (tmtt) cc_final: 0.7485 (tmtt) REVERT: A 309 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6959 (mtm) REVERT: A 320 ARG cc_start: 0.6405 (tpp80) cc_final: 0.5524 (tpp80) REVERT: A 414 MET cc_start: 0.7497 (mmp) cc_final: 0.7168 (mmm) REVERT: A 506 LEU cc_start: 0.7980 (mm) cc_final: 0.7649 (mp) REVERT: A 1004 GLN cc_start: 0.7971 (mp10) cc_final: 0.7394 (mp10) REVERT: A 1009 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 1012 TRP cc_start: 0.8647 (t-100) cc_final: 0.8370 (t-100) REVERT: A 1015 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 1033 ASP cc_start: 0.7902 (t0) cc_final: 0.7534 (t0) REVERT: A 1046 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8178 (mt0) REVERT: A 1079 ASP cc_start: 0.7274 (m-30) cc_final: 0.6969 (m-30) REVERT: A 543 LEU cc_start: 0.7967 (tp) cc_final: 0.7691 (tt) REVERT: A 565 TRP cc_start: 0.6745 (m-10) cc_final: 0.6531 (m-10) REVERT: B 50 TRP cc_start: 0.8587 (t60) cc_final: 0.8303 (t60) REVERT: B 80 ASN cc_start: 0.7957 (t0) cc_final: 0.7670 (t0) REVERT: B 157 LYS cc_start: 0.7744 (tttt) cc_final: 0.7438 (tttt) REVERT: C 32 TYR cc_start: 0.7369 (m-80) cc_final: 0.7033 (m-80) REVERT: C 46 GLU cc_start: 0.6737 (mp0) cc_final: 0.5976 (mp0) REVERT: C 87 LYS cc_start: 0.7059 (tmmt) cc_final: 0.6792 (tmmt) outliers start: 37 outliers final: 28 residues processed: 233 average time/residue: 0.1932 time to fit residues: 60.1927 Evaluate side-chains 245 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 GLN B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134797 restraints weight = 12594.232| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.86 r_work: 0.3557 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7617 Z= 0.163 Angle : 0.588 10.267 10387 Z= 0.292 Chirality : 0.041 0.147 1187 Planarity : 0.005 0.071 1315 Dihedral : 4.145 25.694 1071 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.10 % Allowed : 20.50 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 983 helix: 0.75 (0.30), residues: 327 sheet: -0.13 (0.37), residues: 196 loop : -1.63 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.011 0.001 PHE A 406 TYR 0.020 0.001 TYR A1110 ARG 0.001 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7493 (tmtt) REVERT: A 309 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6818 (mtm) REVERT: A 320 ARG cc_start: 0.6401 (tpp80) cc_final: 0.5537 (tpp80) REVERT: A 414 MET cc_start: 0.7479 (mmp) cc_final: 0.7186 (mmm) REVERT: A 506 LEU cc_start: 0.7932 (mm) cc_final: 0.7650 (mp) REVERT: A 1004 GLN cc_start: 0.7941 (mp10) cc_final: 0.7388 (mp10) REVERT: A 1009 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7807 (mm-30) REVERT: A 1033 ASP cc_start: 0.7895 (t0) cc_final: 0.7532 (t0) REVERT: A 1079 ASP cc_start: 0.7256 (m-30) cc_final: 0.6944 (m-30) REVERT: A 1112 GLU cc_start: 0.8053 (tp30) cc_final: 0.7792 (tp30) REVERT: A 543 LEU cc_start: 0.7968 (tp) cc_final: 0.7686 (tt) REVERT: A 565 TRP cc_start: 0.6697 (m-10) cc_final: 0.6494 (m-10) REVERT: B 39 TRP cc_start: 0.8481 (m100) cc_final: 0.8274 (m100) REVERT: B 80 ASN cc_start: 0.7931 (t0) cc_final: 0.7648 (t0) REVERT: B 157 LYS cc_start: 0.7713 (tttt) cc_final: 0.7408 (tttt) REVERT: C 46 GLU cc_start: 0.6649 (mp0) cc_final: 0.5860 (mp0) REVERT: D 70 THR cc_start: 0.8193 (p) cc_final: 0.7971 (p) REVERT: D 209 LYS cc_start: 0.7755 (mttp) cc_final: 0.7396 (mttp) outliers start: 31 outliers final: 26 residues processed: 231 average time/residue: 0.1893 time to fit residues: 58.2694 Evaluate side-chains 243 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1030 GLN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 95 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN A1046 GLN B 169 ASN D 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133693 restraints weight = 12535.638| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.82 r_work: 0.3557 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7617 Z= 0.198 Angle : 0.601 10.089 10387 Z= 0.301 Chirality : 0.041 0.174 1187 Planarity : 0.005 0.070 1315 Dihedral : 4.182 25.884 1071 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.89 % Allowed : 19.71 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 983 helix: 0.67 (0.30), residues: 326 sheet: -0.15 (0.37), residues: 196 loop : -1.61 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 420 HIS 0.002 0.000 HIS B 38 PHE 0.009 0.001 PHE A 406 TYR 0.020 0.001 TYR A1110 ARG 0.001 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7838 (tmtt) cc_final: 0.7552 (tmtt) REVERT: A 309 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6871 (mtm) REVERT: A 315 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 320 ARG cc_start: 0.6391 (tpp80) cc_final: 0.5543 (tpp80) REVERT: A 414 MET cc_start: 0.7500 (mmp) cc_final: 0.7184 (mmm) REVERT: A 506 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 1004 GLN cc_start: 0.7936 (mp10) cc_final: 0.7368 (mp10) REVERT: A 1009 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 1012 TRP cc_start: 0.8646 (t-100) cc_final: 0.8352 (t-100) REVERT: A 1015 LEU cc_start: 0.8573 (mt) cc_final: 0.7955 (mt) REVERT: A 1033 ASP cc_start: 0.7889 (t0) cc_final: 0.7519 (t0) REVERT: A 1079 ASP cc_start: 0.7298 (m-30) cc_final: 0.7060 (m-30) REVERT: A 1108 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8166 (tp-100) REVERT: A 1112 GLU cc_start: 0.8041 (tp30) cc_final: 0.7803 (tp30) REVERT: B 50 TRP cc_start: 0.8605 (t60) cc_final: 0.8314 (t60) REVERT: B 80 ASN cc_start: 0.7918 (t0) cc_final: 0.7666 (t0) REVERT: B 157 LYS cc_start: 0.7719 (tttt) cc_final: 0.7414 (tttt) REVERT: C 6 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5618 (pt0) REVERT: C 46 GLU cc_start: 0.6690 (mp0) cc_final: 0.5895 (mp0) REVERT: D 209 LYS cc_start: 0.7756 (mttp) cc_final: 0.7399 (mttp) outliers start: 37 outliers final: 28 residues processed: 230 average time/residue: 0.1951 time to fit residues: 59.9734 Evaluate side-chains 241 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.159715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133284 restraints weight = 12662.894| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.86 r_work: 0.3548 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7617 Z= 0.216 Angle : 0.644 10.774 10387 Z= 0.317 Chirality : 0.042 0.160 1187 Planarity : 0.005 0.073 1315 Dihedral : 4.327 30.426 1071 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.76 % Allowed : 20.63 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 983 helix: 0.69 (0.30), residues: 326 sheet: -0.42 (0.36), residues: 216 loop : -1.54 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.009 0.001 PHE A 490 TYR 0.018 0.001 TYR A1110 ARG 0.005 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7862 (tmtt) cc_final: 0.7586 (tmtt) REVERT: A 315 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 320 ARG cc_start: 0.6413 (tpp80) cc_final: 0.5572 (tpp80) REVERT: A 365 VAL cc_start: 0.8002 (p) cc_final: 0.7792 (p) REVERT: A 414 MET cc_start: 0.7529 (mmp) cc_final: 0.7224 (mmm) REVERT: A 433 MET cc_start: 0.7886 (tmm) cc_final: 0.7543 (tmm) REVERT: A 506 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7744 (mp) REVERT: A 1004 GLN cc_start: 0.7958 (mp10) cc_final: 0.7392 (mp10) REVERT: A 1009 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 1012 TRP cc_start: 0.8663 (t-100) cc_final: 0.8382 (t-100) REVERT: A 1033 ASP cc_start: 0.7911 (t0) cc_final: 0.7625 (t0) REVERT: A 1108 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8151 (tp-100) REVERT: B 50 TRP cc_start: 0.8624 (t60) cc_final: 0.8327 (t60) REVERT: B 80 ASN cc_start: 0.7943 (t0) cc_final: 0.7711 (t0) REVERT: B 157 LYS cc_start: 0.7695 (tttt) cc_final: 0.7402 (tttt) REVERT: C 6 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5581 (pt0) REVERT: C 46 GLU cc_start: 0.6715 (mp0) cc_final: 0.5916 (mp0) REVERT: C 68 PHE cc_start: 0.7171 (m-80) cc_final: 0.6853 (m-80) REVERT: D 209 LYS cc_start: 0.7749 (mttp) cc_final: 0.7391 (mttp) outliers start: 36 outliers final: 32 residues processed: 231 average time/residue: 0.2042 time to fit residues: 63.2052 Evaluate side-chains 253 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 GLN B 169 ASN C 1 GLN D 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.159678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133338 restraints weight = 12653.102| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.85 r_work: 0.3535 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7617 Z= 0.202 Angle : 0.626 10.366 10387 Z= 0.311 Chirality : 0.041 0.183 1187 Planarity : 0.005 0.074 1315 Dihedral : 4.270 27.886 1071 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.89 % Allowed : 20.90 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 983 helix: 0.75 (0.30), residues: 326 sheet: -0.38 (0.36), residues: 216 loop : -1.51 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 435 HIS 0.002 0.001 HIS B 214 PHE 0.008 0.001 PHE A1066 TYR 0.039 0.001 TYR D 50 ARG 0.002 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7882 (tmtt) cc_final: 0.7636 (tmtt) REVERT: A 315 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 320 ARG cc_start: 0.6447 (tpp80) cc_final: 0.5608 (tpp80) REVERT: A 365 VAL cc_start: 0.7989 (p) cc_final: 0.7782 (p) REVERT: A 414 MET cc_start: 0.7516 (mmp) cc_final: 0.7193 (mmm) REVERT: A 433 MET cc_start: 0.7908 (tmm) cc_final: 0.7222 (tmm) REVERT: A 443 ASN cc_start: 0.6999 (m-40) cc_final: 0.6525 (t0) REVERT: A 506 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7738 (mp) REVERT: A 1004 GLN cc_start: 0.7950 (mp10) cc_final: 0.7373 (mp10) REVERT: A 1009 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 1012 TRP cc_start: 0.8649 (t-100) cc_final: 0.8337 (t-100) REVERT: A 1015 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 1033 ASP cc_start: 0.7951 (t0) cc_final: 0.7612 (t0) REVERT: A 1108 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8118 (tp-100) REVERT: B 50 TRP cc_start: 0.8617 (t60) cc_final: 0.8325 (t60) REVERT: B 80 ASN cc_start: 0.7949 (t0) cc_final: 0.7737 (t0) REVERT: B 157 LYS cc_start: 0.7669 (tttt) cc_final: 0.7380 (tttt) REVERT: C 6 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.5587 (pt0) REVERT: C 27 ARG cc_start: 0.5985 (mtt90) cc_final: 0.4949 (mtt90) REVERT: C 46 GLU cc_start: 0.6698 (mp0) cc_final: 0.5885 (mp0) REVERT: C 68 PHE cc_start: 0.7191 (m-80) cc_final: 0.6859 (m-80) REVERT: D 209 LYS cc_start: 0.7742 (mttp) cc_final: 0.7364 (mttp) outliers start: 37 outliers final: 33 residues processed: 232 average time/residue: 0.1962 time to fit residues: 60.1456 Evaluate side-chains 251 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.379 > 50: distance: 35 - 36: 3.782 distance: 39 - 40: 7.649 distance: 40 - 41: 4.105 distance: 40 - 43: 9.101 distance: 41 - 42: 7.371 distance: 43 - 44: 13.603 distance: 44 - 45: 16.225 distance: 44 - 46: 14.616 distance: 45 - 47: 8.714 distance: 46 - 48: 9.411 distance: 47 - 48: 9.342 distance: 49 - 50: 4.320 distance: 50 - 51: 14.001 distance: 50 - 53: 7.294 distance: 51 - 52: 7.849 distance: 51 - 54: 4.371 distance: 54 - 55: 8.338 distance: 55 - 56: 12.202 distance: 55 - 58: 9.060 distance: 56 - 57: 8.175 distance: 56 - 59: 11.613 distance: 59 - 60: 21.649 distance: 60 - 63: 12.752 distance: 61 - 62: 30.537 distance: 61 - 67: 25.218 distance: 63 - 64: 33.630 distance: 63 - 65: 27.937 distance: 64 - 66: 7.095 distance: 67 - 68: 19.068 distance: 68 - 69: 7.029 distance: 68 - 71: 29.521 distance: 69 - 70: 30.042 distance: 69 - 76: 9.532 distance: 71 - 72: 23.704 distance: 72 - 73: 7.150 distance: 73 - 74: 11.200 distance: 73 - 75: 17.114 distance: 76 - 77: 5.243 distance: 77 - 78: 19.306 distance: 77 - 80: 22.690 distance: 78 - 79: 15.634 distance: 78 - 81: 4.902 distance: 81 - 82: 4.669 distance: 82 - 83: 4.387 distance: 82 - 85: 3.342 distance: 83 - 84: 10.239 distance: 83 - 89: 5.189 distance: 84 - 108: 11.092 distance: 85 - 86: 8.953 distance: 86 - 87: 5.582 distance: 89 - 90: 6.311 distance: 90 - 91: 9.743 distance: 90 - 93: 5.645 distance: 91 - 92: 3.325 distance: 91 - 95: 12.139 distance: 92 - 119: 10.547 distance: 93 - 94: 9.053 distance: 95 - 96: 4.226 distance: 96 - 97: 7.932 distance: 96 - 99: 14.492 distance: 97 - 98: 8.888 distance: 97 - 100: 7.395 distance: 98 - 128: 5.280