Starting phenix.real_space_refine on Sun May 11 04:02:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9o_36112/05_2025/8j9o_36112_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9o_36112/05_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_36112/05_2025/8j9o_36112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9o_36112/05_2025/8j9o_36112.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9o_36112/05_2025/8j9o_36112_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9o_36112/05_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-5687/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: 4.76, per 1000 atoms: 0.64 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 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: 0.91 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: 2.27 Time building geometry restraints manager: 2.13 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: 1.440 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.520 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- 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 7625 Z= 0.151 Angle : 0.748 10.744 10403 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 Details of bonding type rmsd hydrogen bonds : bond 0.23769 ( 324) hydrogen bonds : angle 7.79979 ( 945) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.69006 ( 16) covalent geometry : bond 0.00326 ( 7617) covalent geometry : angle 0.74788 (10387) *********************** 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 : 0.715 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: 0.1922 time to fit residues: 57.2506 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 : 0.782 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127980 restraints weight = 12562.312| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.81 r_work: 0.3519 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 7625 Z= 0.256 Angle : 0.674 9.769 10403 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 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 324) hydrogen bonds : angle 5.48856 ( 945) SS BOND : bond 0.00304 ( 8) SS BOND : angle 0.92986 ( 16) covalent geometry : bond 0.00558 ( 7617) covalent geometry : angle 0.67393 (10387) *********************** 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 : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 PHE cc_start: 0.6836 (t80) cc_final: 0.6622 (t80) REVERT: A 294 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7413 (tmtt) REVERT: A 320 ARG cc_start: 0.6329 (tpp80) cc_final: 0.5466 (tpp80) REVERT: A 506 LEU cc_start: 0.8073 (mm) cc_final: 0.7756 (mp) REVERT: A 1004 GLN cc_start: 0.7993 (mp10) cc_final: 0.7459 (mp10) REVERT: A 1012 TRP cc_start: 0.8783 (t-100) cc_final: 0.8457 (t-100) REVERT: A 1018 ASN cc_start: 0.7602 (m110) cc_final: 0.7250 (m110) REVERT: A 1033 ASP cc_start: 0.7897 (t0) cc_final: 0.7549 (t0) REVERT: A 543 LEU cc_start: 0.7996 (tp) cc_final: 0.7726 (tt) REVERT: B 80 ASN cc_start: 0.7961 (t0) cc_final: 0.7612 (t0) REVERT: B 157 LYS cc_start: 0.7746 (tttt) cc_final: 0.7425 (tttt) REVERT: C 32 TYR cc_start: 0.7471 (m-80) cc_final: 0.7109 (m-80) REVERT: C 46 GLU cc_start: 0.6834 (mp0) cc_final: 0.6112 (mp0) outliers start: 21 outliers final: 14 residues processed: 226 average time/residue: 0.1906 time to fit residues: 57.3125 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 : 0.716 ------------------------------------------------------------------------------- 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: 3.9990 chunk 67 optimal weight: 0.0010 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.157885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130400 restraints weight = 12788.689| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.89 r_work: 0.3552 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7625 Z= 0.128 Angle : 0.602 9.693 10403 Z= 0.303 Chirality : 0.041 0.135 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.322 27.692 1071 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.44 % Allowed : 14.55 % Favored : 82.01 % 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: -1.14 (0.26), residues: 983 helix: 0.28 (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 0.006 0.001 TRP A 420 HIS 0.002 0.000 HIS B 38 PHE 0.012 0.001 PHE A1066 TYR 0.017 0.001 TYR A1110 ARG 0.002 0.000 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 324) hydrogen bonds : angle 4.98147 ( 945) SS BOND : bond 0.00202 ( 8) SS BOND : angle 0.70405 ( 16) covalent geometry : bond 0.00286 ( 7617) covalent geometry : angle 0.60203 (10387) *********************** 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 257 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7400 (tmtt) REVERT: A 309 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6847 (mtm) REVERT: A 320 ARG cc_start: 0.6329 (tpp80) cc_final: 0.5476 (tpp80) REVERT: A 443 ASN cc_start: 0.6973 (m-40) cc_final: 0.6500 (t0) REVERT: A 506 LEU cc_start: 0.7986 (mm) cc_final: 0.7694 (mp) REVERT: A 1004 GLN cc_start: 0.7959 (mp10) cc_final: 0.7394 (mp10) REVERT: A 1018 ASN cc_start: 0.7447 (m110) cc_final: 0.7111 (m110) REVERT: A 1033 ASP cc_start: 0.7878 (t0) cc_final: 0.7528 (t0) REVERT: A 1078 ASP cc_start: 0.7326 (m-30) cc_final: 0.7121 (m-30) REVERT: A 1079 ASP cc_start: 0.7167 (m-30) cc_final: 0.6948 (m-30) REVERT: A 543 LEU cc_start: 0.7972 (tp) cc_final: 0.7693 (tt) REVERT: B 50 TRP cc_start: 0.8573 (t60) cc_final: 0.8071 (t60) REVERT: B 80 ASN cc_start: 0.7907 (t0) cc_final: 0.7547 (t0) REVERT: B 157 LYS cc_start: 0.7742 (tttt) cc_final: 0.7426 (tttt) REVERT: C 32 TYR cc_start: 0.7406 (m-80) cc_final: 0.7064 (m-80) REVERT: C 46 GLU cc_start: 0.6740 (mp0) cc_final: 0.6016 (mp0) outliers start: 26 outliers final: 17 residues processed: 236 average time/residue: 0.1861 time to fit residues: 58.8452 Evaluate side-chains 239 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 130 THR 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 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: 0.5980 chunk 58 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.156472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129205 restraints weight = 12686.677| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.86 r_work: 0.3544 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7625 Z= 0.149 Angle : 0.611 9.632 10403 Z= 0.306 Chirality : 0.041 0.141 1187 Planarity : 0.005 0.062 1315 Dihedral : 4.264 27.561 1071 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.50 % Allowed : 17.33 % Favored : 78.17 % 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: -1.04 (0.27), residues: 983 helix: 0.49 (0.29), residues: 326 sheet: -0.61 (0.35), residues: 221 loop : -1.63 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.010 0.001 PHE A1066 TYR 0.022 0.001 TYR C 104 ARG 0.002 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 324) hydrogen bonds : angle 4.76167 ( 945) SS BOND : bond 0.00181 ( 8) SS BOND : angle 0.68212 ( 16) covalent geometry : bond 0.00331 ( 7617) covalent geometry : angle 0.61129 (10387) *********************** 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 263 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7468 (tmtt) REVERT: A 309 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.6950 (mtm) REVERT: A 320 ARG cc_start: 0.6389 (tpp80) cc_final: 0.5507 (tpp80) REVERT: A 414 MET cc_start: 0.7532 (mmp) cc_final: 0.7145 (mmm) REVERT: A 506 LEU cc_start: 0.8000 (mm) cc_final: 0.7665 (mp) REVERT: A 1004 GLN cc_start: 0.7971 (mp10) cc_final: 0.7438 (mp10) REVERT: A 1009 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 1018 ASN cc_start: 0.7453 (m110) cc_final: 0.7212 (m110) REVERT: A 1033 ASP cc_start: 0.7898 (t0) cc_final: 0.7529 (t0) REVERT: A 1079 ASP cc_start: 0.7272 (m-30) cc_final: 0.7022 (m-30) REVERT: A 543 LEU cc_start: 0.7954 (tp) cc_final: 0.7668 (tt) REVERT: A 565 TRP cc_start: 0.6848 (m-10) cc_final: 0.6617 (m-10) REVERT: B 50 TRP cc_start: 0.8592 (t60) cc_final: 0.8301 (t60) REVERT: B 80 ASN cc_start: 0.7949 (t0) cc_final: 0.7637 (t0) REVERT: B 157 LYS cc_start: 0.7744 (tttt) cc_final: 0.7444 (tttt) REVERT: C 32 TYR cc_start: 0.7421 (m-80) cc_final: 0.7082 (m-80) REVERT: C 46 GLU cc_start: 0.6785 (mp0) cc_final: 0.6019 (mp0) outliers start: 34 outliers final: 25 residues processed: 240 average time/residue: 0.1943 time to fit residues: 62.6327 Evaluate side-chains 251 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 462 ILE 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 503 THR 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 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 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: 0.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 96 optimal weight: 0.0070 chunk 86 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** A1046 GLN B 169 ASN D 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.159916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133323 restraints weight = 12566.033| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.84 r_work: 0.3552 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7625 Z= 0.137 Angle : 0.605 9.821 10403 Z= 0.302 Chirality : 0.041 0.137 1187 Planarity : 0.005 0.062 1315 Dihedral : 4.231 26.936 1071 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.50 % Allowed : 19.05 % Favored : 76.46 % 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: -0.91 (0.27), residues: 983 helix: 0.65 (0.29), residues: 326 sheet: -0.39 (0.36), residues: 201 loop : -1.64 (0.28), residues: 456 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 0.009 0.001 PHE A1066 TYR 0.021 0.001 TYR A1110 ARG 0.002 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 324) hydrogen bonds : angle 4.64022 ( 945) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.65767 ( 16) covalent geometry : bond 0.00308 ( 7617) covalent geometry : angle 0.60518 (10387) *********************** 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 260 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7481 (tmtt) REVERT: A 309 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.6930 (mtm) REVERT: A 320 ARG cc_start: 0.6387 (tpp80) cc_final: 0.5518 (tpp80) REVERT: A 414 MET cc_start: 0.7498 (mmp) cc_final: 0.7178 (mmm) REVERT: A 501 ILE cc_start: 0.7934 (mt) cc_final: 0.7671 (mt) REVERT: A 506 LEU cc_start: 0.7984 (mm) cc_final: 0.7655 (mp) REVERT: A 1004 GLN cc_start: 0.7977 (mp10) cc_final: 0.7394 (mp10) REVERT: A 1009 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 1012 TRP cc_start: 0.8644 (t-100) cc_final: 0.8414 (t-100) REVERT: A 1018 ASN cc_start: 0.7433 (m110) cc_final: 0.7184 (m110) REVERT: A 1033 ASP cc_start: 0.7920 (t0) cc_final: 0.7543 (t0) REVERT: A 1079 ASP cc_start: 0.7262 (m-30) cc_final: 0.7025 (m-30) REVERT: B 50 TRP cc_start: 0.8595 (t60) cc_final: 0.8310 (t60) REVERT: B 80 ASN cc_start: 0.7955 (t0) cc_final: 0.7664 (t0) REVERT: B 157 LYS cc_start: 0.7743 (tttt) cc_final: 0.7436 (tttt) REVERT: C 32 TYR cc_start: 0.7375 (m-80) cc_final: 0.7031 (m-80) REVERT: C 46 GLU cc_start: 0.6700 (mp0) cc_final: 0.5931 (mp0) outliers start: 34 outliers final: 29 residues processed: 236 average time/residue: 0.1878 time to fit residues: 59.6580 Evaluate side-chains 253 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 462 ILE 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 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 37 LEU Chi-restraints excluded: chain B residue 56 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 164 VAL 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: 2.9990 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 24 optimal weight: 0.0470 chunk 55 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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** B 169 ASN D 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.161104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134502 restraints weight = 12578.939| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.87 r_work: 0.3568 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7625 Z= 0.112 Angle : 0.595 10.231 10403 Z= 0.294 Chirality : 0.040 0.137 1187 Planarity : 0.005 0.066 1315 Dihedral : 4.092 26.169 1071 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.37 % Allowed : 19.97 % Favored : 75.66 % 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: -0.73 (0.27), residues: 983 helix: 0.77 (0.30), residues: 326 sheet: -0.13 (0.37), residues: 196 loop : -1.58 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 420 HIS 0.002 0.000 HIS B 38 PHE 0.012 0.001 PHE A 406 TYR 0.033 0.001 TYR D 50 ARG 0.001 0.000 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 324) hydrogen bonds : angle 4.47312 ( 945) SS BOND : bond 0.00174 ( 8) SS BOND : angle 0.58359 ( 16) covalent geometry : bond 0.00249 ( 7617) covalent geometry : angle 0.59497 (10387) *********************** 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 258 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7798 (tmtt) cc_final: 0.7501 (tmtt) REVERT: A 309 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6824 (mtm) REVERT: A 320 ARG cc_start: 0.6405 (tpp80) cc_final: 0.5540 (tpp80) REVERT: A 365 VAL cc_start: 0.7900 (p) cc_final: 0.7682 (p) REVERT: A 414 MET cc_start: 0.7504 (mmp) cc_final: 0.7203 (mmm) REVERT: A 501 ILE cc_start: 0.7893 (mt) cc_final: 0.7644 (mt) REVERT: A 506 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 1004 GLN cc_start: 0.7922 (mp10) cc_final: 0.7374 (mp10) REVERT: A 1009 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 1012 TRP cc_start: 0.8623 (t-100) cc_final: 0.8355 (t-100) REVERT: A 1015 LEU cc_start: 0.8547 (mt) cc_final: 0.7942 (mt) REVERT: A 1018 ASN cc_start: 0.7380 (m110) cc_final: 0.7137 (m110) REVERT: A 1033 ASP cc_start: 0.7894 (t0) cc_final: 0.7527 (t0) REVERT: A 1112 GLU cc_start: 0.8051 (tp30) cc_final: 0.7791 (tp30) REVERT: B 39 TRP cc_start: 0.8479 (m100) cc_final: 0.8278 (m100) REVERT: B 80 ASN cc_start: 0.7922 (t0) cc_final: 0.7644 (t0) REVERT: B 157 LYS cc_start: 0.7706 (tttt) cc_final: 0.7413 (tttt) REVERT: C 6 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.5551 (pt0) REVERT: C 46 GLU cc_start: 0.6637 (mp0) cc_final: 0.5845 (mp0) REVERT: D 70 THR cc_start: 0.8180 (p) cc_final: 0.7953 (p) REVERT: D 209 LYS cc_start: 0.7749 (mttp) cc_final: 0.7387 (mttp) outliers start: 33 outliers final: 25 residues processed: 236 average time/residue: 0.1978 time to fit residues: 62.2142 Evaluate side-chains 251 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 413 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 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 B residue 56 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 197 THR Chi-restraints excluded: chain B residue 211 ASN 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 4 GLN 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: 2.9990 chunk 71 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1030 GLN 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 = 0.4078 r_free = 0.4078 target = 0.159215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132576 restraints weight = 12527.131| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.85 r_work: 0.3542 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7625 Z= 0.159 Angle : 0.621 10.171 10403 Z= 0.309 Chirality : 0.042 0.143 1187 Planarity : 0.005 0.066 1315 Dihedral : 4.218 27.090 1071 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.50 % Allowed : 20.37 % Favored : 75.13 % 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: -0.82 (0.27), residues: 983 helix: 0.73 (0.29), residues: 326 sheet: -0.52 (0.35), residues: 223 loop : -1.53 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.010 0.001 PHE A 406 TYR 0.027 0.001 TYR D 50 ARG 0.001 0.000 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 324) hydrogen bonds : angle 4.57136 ( 945) SS BOND : bond 0.00177 ( 8) SS BOND : angle 0.71051 ( 16) covalent geometry : bond 0.00355 ( 7617) covalent geometry : angle 0.62064 (10387) *********************** 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 264 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7861 (tmtt) cc_final: 0.7587 (tmtt) REVERT: A 309 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6901 (mtm) REVERT: A 320 ARG cc_start: 0.6410 (tpp80) cc_final: 0.5560 (tpp80) REVERT: A 365 VAL cc_start: 0.8025 (p) cc_final: 0.7810 (p) REVERT: A 414 MET cc_start: 0.7536 (mmp) cc_final: 0.7220 (mmm) REVERT: A 443 ASN cc_start: 0.7048 (m-40) cc_final: 0.6584 (t0) REVERT: A 506 LEU cc_start: 0.8007 (mm) cc_final: 0.7683 (mp) REVERT: A 1004 GLN cc_start: 0.7986 (mp10) cc_final: 0.7401 (mp10) REVERT: A 1009 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 1012 TRP cc_start: 0.8670 (t-100) cc_final: 0.8374 (t-100) REVERT: A 1015 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7991 (mt) REVERT: A 1033 ASP cc_start: 0.7930 (t0) cc_final: 0.7673 (t0) REVERT: A 1108 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8121 (tp-100) REVERT: A 1112 GLU cc_start: 0.8067 (tp30) cc_final: 0.7861 (tp30) REVERT: B 50 TRP cc_start: 0.8628 (t60) cc_final: 0.8329 (t60) REVERT: B 80 ASN cc_start: 0.7948 (t0) cc_final: 0.7706 (t0) REVERT: B 157 LYS cc_start: 0.7719 (tttt) cc_final: 0.7423 (tttt) REVERT: C 46 GLU cc_start: 0.6762 (mp0) cc_final: 0.5943 (mp0) REVERT: C 68 PHE cc_start: 0.7195 (m-80) cc_final: 0.6868 (m-80) REVERT: C 87 LYS cc_start: 0.7087 (tmmt) cc_final: 0.6817 (tmmt) REVERT: D 209 LYS cc_start: 0.7764 (mttp) cc_final: 0.7421 (mttp) outliers start: 34 outliers final: 30 residues processed: 239 average time/residue: 0.2011 time to fit residues: 64.9115 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 : 0.761 ------------------------------------------------------------------------------- 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 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 422 ILE 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 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1030 GLN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1038 MET 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 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 197 THR 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 177 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 GLN B 169 ASN D 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.159983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132779 restraints weight = 12626.426| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.94 r_work: 0.3538 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7625 Z= 0.151 Angle : 0.628 10.633 10403 Z= 0.312 Chirality : 0.042 0.196 1187 Planarity : 0.005 0.069 1315 Dihedral : 4.245 27.047 1071 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.16 % Allowed : 20.37 % Favored : 74.47 % 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: -0.78 (0.27), residues: 983 helix: 0.74 (0.30), residues: 326 sheet: -0.47 (0.35), residues: 216 loop : -1.49 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.008 0.001 PHE A1066 TYR 0.036 0.001 TYR D 50 ARG 0.001 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 324) hydrogen bonds : angle 4.58940 ( 945) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.77106 ( 16) covalent geometry : bond 0.00335 ( 7617) covalent geometry : angle 0.62782 (10387) *********************** 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 271 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7618 (tmtt) REVERT: A 315 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 320 ARG cc_start: 0.6425 (tpp80) cc_final: 0.5587 (tpp80) REVERT: A 365 VAL cc_start: 0.8014 (p) cc_final: 0.7801 (p) REVERT: A 414 MET cc_start: 0.7538 (mmp) cc_final: 0.7242 (mmm) REVERT: A 443 ASN cc_start: 0.7089 (m-40) cc_final: 0.6591 (t0) REVERT: A 454 VAL cc_start: 0.7197 (OUTLIER) cc_final: 0.6790 (m) REVERT: A 506 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 1004 GLN cc_start: 0.8011 (mp10) cc_final: 0.7402 (mp10) REVERT: A 1009 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 1012 TRP cc_start: 0.8647 (t-100) cc_final: 0.8391 (t-100) REVERT: A 1015 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 1033 ASP cc_start: 0.8022 (t0) cc_final: 0.7693 (t0) REVERT: A 1035 LEU cc_start: 0.8599 (mt) cc_final: 0.8385 (mt) REVERT: A 1108 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8111 (tp-100) REVERT: B 50 TRP cc_start: 0.8628 (t60) cc_final: 0.8335 (t60) REVERT: B 80 ASN cc_start: 0.7973 (t0) cc_final: 0.7730 (t0) REVERT: B 157 LYS cc_start: 0.7692 (tttt) cc_final: 0.7397 (tttt) REVERT: C 6 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5675 (pt0) REVERT: C 46 GLU cc_start: 0.6759 (mp0) cc_final: 0.5932 (mp0) REVERT: C 68 PHE cc_start: 0.7193 (m-80) cc_final: 0.6871 (m-80) REVERT: C 87 LYS cc_start: 0.7047 (tmmt) cc_final: 0.6822 (tmmt) REVERT: D 209 LYS cc_start: 0.7755 (mttp) cc_final: 0.7370 (mttp) outliers start: 39 outliers final: 32 residues processed: 245 average time/residue: 0.1989 time to fit residues: 64.8713 Evaluate side-chains 262 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 422 ILE 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 479 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 THR 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 92 GLU Chi-restraints excluded: chain B residue 99 CYS 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 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 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: 3.9990 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 0.0060 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.0000 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4086 r_free = 0.4086 target = 0.159960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133246 restraints weight = 12678.477| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.90 r_work: 0.3556 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7625 Z= 0.123 Angle : 0.610 11.233 10403 Z= 0.301 Chirality : 0.041 0.141 1187 Planarity : 0.005 0.071 1315 Dihedral : 4.151 26.373 1071 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.03 % Allowed : 21.16 % Favored : 73.81 % 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: -0.71 (0.27), residues: 983 helix: 0.81 (0.30), residues: 326 sheet: -0.42 (0.36), residues: 216 loop : -1.47 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.002 0.001 HIS B 214 PHE 0.008 0.001 PHE A 406 TYR 0.037 0.001 TYR D 50 ARG 0.004 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 324) hydrogen bonds : angle 4.50375 ( 945) SS BOND : bond 0.00174 ( 8) SS BOND : angle 0.66458 ( 16) covalent geometry : bond 0.00274 ( 7617) covalent geometry : angle 0.61017 (10387) *********************** 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 264 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7628 (tmtt) REVERT: A 315 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 365 VAL cc_start: 0.7984 (p) cc_final: 0.7774 (p) REVERT: A 414 MET cc_start: 0.7488 (mmp) cc_final: 0.7194 (mmm) REVERT: A 443 ASN cc_start: 0.7048 (m-40) cc_final: 0.6568 (t0) REVERT: A 501 ILE cc_start: 0.7884 (mt) cc_final: 0.7672 (mt) REVERT: A 506 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 1004 GLN cc_start: 0.7960 (mp10) cc_final: 0.7375 (mp10) REVERT: A 1009 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 1012 TRP cc_start: 0.8635 (t-100) cc_final: 0.8328 (t-100) REVERT: A 1015 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 1033 ASP cc_start: 0.7969 (t0) cc_final: 0.7628 (t0) REVERT: A 1098 GLN cc_start: 0.8078 (pt0) cc_final: 0.7634 (pp30) REVERT: A 1108 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8120 (tp-100) REVERT: B 80 ASN cc_start: 0.7946 (t0) cc_final: 0.7723 (t0) REVERT: B 157 LYS cc_start: 0.7658 (tttt) cc_final: 0.7372 (tttt) REVERT: C 6 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5650 (pt0) REVERT: C 32 TYR cc_start: 0.7398 (m-80) cc_final: 0.6996 (m-80) REVERT: C 46 GLU cc_start: 0.6708 (mp0) cc_final: 0.5888 (mp0) REVERT: C 68 PHE cc_start: 0.7157 (m-80) cc_final: 0.6860 (m-80) REVERT: C 87 LYS cc_start: 0.6981 (tmmt) cc_final: 0.6753 (tmmt) REVERT: D 209 LYS cc_start: 0.7711 (mttp) cc_final: 0.7333 (mttp) outliers start: 38 outliers final: 33 residues processed: 241 average time/residue: 0.1885 time to fit residues: 60.4812 Evaluate side-chains 260 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 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 1038 MET 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 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 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 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 ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 20 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 GLN B 169 ASN D 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133348 restraints weight = 12636.205| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.95 r_work: 0.3544 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7625 Z= 0.131 Angle : 0.624 10.895 10403 Z= 0.309 Chirality : 0.041 0.145 1187 Planarity : 0.005 0.073 1315 Dihedral : 4.146 26.173 1071 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.63 % Allowed : 21.83 % Favored : 73.54 % 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: -0.71 (0.27), residues: 983 helix: 0.81 (0.30), residues: 326 sheet: -0.41 (0.36), residues: 216 loop : -1.47 (0.30), residues: 441 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 0.007 0.001 PHE A1066 TYR 0.033 0.001 TYR D 50 ARG 0.013 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 324) hydrogen bonds : angle 4.52041 ( 945) SS BOND : bond 0.00193 ( 8) SS BOND : angle 0.58801 ( 16) covalent geometry : bond 0.00289 ( 7617) covalent geometry : angle 0.62434 (10387) ********************** REFINEMENT MACRO_CYCLE 10 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 260 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7884 (tmtt) cc_final: 0.7639 (tmtt) REVERT: A 315 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7007 (mt-10) REVERT: A 365 VAL cc_start: 0.7958 (p) cc_final: 0.7752 (p) REVERT: A 414 MET cc_start: 0.7508 (mmp) cc_final: 0.7211 (mmm) REVERT: A 443 ASN cc_start: 0.7073 (m-40) cc_final: 0.6580 (t0) REVERT: A 506 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 1004 GLN cc_start: 0.7983 (mp10) cc_final: 0.7392 (mp10) REVERT: A 1009 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 1015 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 1033 ASP cc_start: 0.7988 (t0) cc_final: 0.7652 (t0) REVERT: A 1098 GLN cc_start: 0.8102 (pt0) cc_final: 0.7646 (pp30) REVERT: A 1108 GLN cc_start: 0.8372 (tp-100) cc_final: 0.8164 (tp-100) REVERT: B 157 LYS cc_start: 0.7642 (tttt) cc_final: 0.7360 (tttt) REVERT: C 6 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5608 (pt0) REVERT: C 46 GLU cc_start: 0.6709 (mp0) cc_final: 0.5876 (mp0) REVERT: C 68 PHE cc_start: 0.7192 (m-80) cc_final: 0.6868 (m-80) REVERT: D 209 LYS cc_start: 0.7699 (mttp) cc_final: 0.7313 (mttp) outliers start: 35 outliers final: 31 residues processed: 240 average time/residue: 0.1973 time to fit residues: 63.0970 Evaluate side-chains 257 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 413 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 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 1038 MET 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 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 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 74 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 ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1030 GLN A1046 GLN B 80 ASN B 169 ASN D 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.160194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133176 restraints weight = 12468.492| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.91 r_work: 0.3537 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7625 Z= 0.151 Angle : 0.642 10.271 10403 Z= 0.319 Chirality : 0.041 0.149 1187 Planarity : 0.005 0.074 1315 Dihedral : 4.195 26.449 1071 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.03 % Allowed : 21.96 % Favored : 73.02 % 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: -0.80 (0.27), residues: 983 helix: 0.78 (0.30), residues: 326 sheet: -0.53 (0.35), residues: 221 loop : -1.52 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 PHE 0.008 0.001 PHE A 490 TYR 0.034 0.001 TYR D 50 ARG 0.009 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 324) hydrogen bonds : angle 4.56458 ( 945) SS BOND : bond 0.00205 ( 8) SS BOND : angle 0.54425 ( 16) covalent geometry : bond 0.00336 ( 7617) covalent geometry : angle 0.64234 (10387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.28 seconds wall clock time: 66 minutes 34.42 seconds (3994.42 seconds total)