Starting phenix.real_space_refine on Fri Aug 22 19:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9o_36112/08_2025/8j9o_36112_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9o_36112/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j9o_36112/08_2025/8j9o_36112_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9o_36112/08_2025/8j9o_36112_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9o_36112/08_2025/8j9o_36112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9o_36112/08_2025/8j9o_36112.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 4, 'ARG:plan': 7, 'GLU:plan': 8, 'GLN:plan1': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1} 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, 'ARG:plan': 1, 'TYR: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, 'ASP:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 1.63, per 1000 atoms: 0.22 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: 0.43 Conformation dependent library (CDL) restraints added in 338.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.16 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: 0.87 Time building geometry restraints manager: 0.57 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.110 ------------------------------------------------------------------------------- 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 : 7.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG D 110 TYR 0.016 0.001 TYR D 92 PHE 0.014 0.001 PHE A 561 TRP 0.009 0.001 TRP B 50 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7617) covalent geometry : angle 0.74788 (10387) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.69006 ( 16) hydrogen bonds : bond 0.23769 ( 324) hydrogen bonds : angle 7.79979 ( 945) *********************** 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 : 0.211 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: 0.0701 time to fit residues: 21.1090 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 6.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN C 39 GLN D 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.162713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136054 restraints weight = 12624.883| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.88 r_work: 0.3595 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7625 Z= 0.117 Angle : 0.597 8.495 10403 Z= 0.304 Chirality : 0.040 0.134 1187 Planarity : 0.005 0.072 1315 Dihedral : 4.205 28.383 1071 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.98 % Allowed : 11.64 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.26), residues: 983 helix: 0.02 (0.29), residues: 325 sheet: -0.43 (0.35), residues: 218 loop : -1.66 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.016 0.001 TYR A 306 PHE 0.014 0.001 PHE A1066 TRP 0.007 0.001 TRP A 420 HIS 0.001 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7617) covalent geometry : angle 0.59716 (10387) SS BOND : bond 0.00224 ( 8) SS BOND : angle 0.69110 ( 16) hydrogen bonds : bond 0.04610 ( 324) hydrogen bonds : angle 5.34737 ( 945) *********************** 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 232 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 PHE cc_start: 0.6709 (t80) cc_final: 0.6492 (t80) REVERT: A 294 LYS cc_start: 0.7624 (tmtt) cc_final: 0.7306 (tmtt) REVERT: A 501 ILE cc_start: 0.7904 (mt) cc_final: 0.7621 (mt) REVERT: A 506 LEU cc_start: 0.7912 (mm) cc_final: 0.7651 (mp) REVERT: A 1004 GLN cc_start: 0.7989 (mp10) cc_final: 0.7403 (mp10) REVERT: A 1018 ASN cc_start: 0.7481 (m110) cc_final: 0.7122 (m110) REVERT: A 1033 ASP cc_start: 0.7838 (t0) cc_final: 0.7488 (t0) REVERT: A 1079 ASP cc_start: 0.6961 (m-30) cc_final: 0.6749 (m-30) REVERT: B 80 ASN cc_start: 0.7753 (t0) cc_final: 0.7383 (t0) REVERT: B 157 LYS cc_start: 0.7738 (tttt) cc_final: 0.7413 (tttt) REVERT: C 32 TYR cc_start: 0.7422 (m-80) cc_final: 0.6948 (m-80) REVERT: C 39 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.4940 (pp30) REVERT: C 46 GLU cc_start: 0.6744 (mp0) cc_final: 0.6031 (mp0) outliers start: 15 outliers final: 7 residues processed: 220 average time/residue: 0.0695 time to fit residues: 20.3623 Evaluate side-chains 217 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.0020 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 A1016 ASN B 169 ASN 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 = 0.160297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133532 restraints weight = 12534.944| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.84 r_work: 0.3557 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7625 Z= 0.164 Angle : 0.625 9.680 10403 Z= 0.315 Chirality : 0.041 0.132 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.195 27.821 1071 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.31 % Allowed : 14.95 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.27), residues: 983 helix: 0.32 (0.29), residues: 326 sheet: -0.66 (0.36), residues: 217 loop : -1.65 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.019 0.001 TYR C 104 PHE 0.012 0.001 PHE A1066 TRP 0.007 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7617) covalent geometry : angle 0.62512 (10387) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.81787 ( 16) hydrogen bonds : bond 0.03891 ( 324) hydrogen bonds : angle 4.89884 ( 945) *********************** 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 249 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7368 (tmtt) REVERT: A 320 ARG cc_start: 0.6384 (tpp80) cc_final: 0.5515 (tpp80) REVERT: A 395 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6707 (mt0) REVERT: A 443 ASN cc_start: 0.6937 (m-40) cc_final: 0.6462 (t0) REVERT: A 473 LEU cc_start: 0.8175 (mp) cc_final: 0.7941 (mp) REVERT: A 506 LEU cc_start: 0.7942 (mm) cc_final: 0.7644 (mp) REVERT: A 1004 GLN cc_start: 0.7958 (mp10) cc_final: 0.7369 (mp10) REVERT: A 1016 ASN cc_start: 0.7046 (m-40) cc_final: 0.5475 (m110) REVERT: A 1018 ASN cc_start: 0.7476 (m110) cc_final: 0.7157 (m110) REVERT: A 1033 ASP cc_start: 0.7896 (t0) cc_final: 0.7551 (t0) REVERT: A 1046 GLN cc_start: 0.8368 (mm110) cc_final: 0.8126 (mm-40) REVERT: A 1078 ASP cc_start: 0.7324 (m-30) cc_final: 0.7115 (m-30) REVERT: A 543 LEU cc_start: 0.7968 (tp) cc_final: 0.7694 (tt) REVERT: B 50 TRP cc_start: 0.8576 (t60) cc_final: 0.8106 (t60) REVERT: B 80 ASN cc_start: 0.7900 (t0) cc_final: 0.7548 (t0) REVERT: B 157 LYS cc_start: 0.7754 (tttt) cc_final: 0.7436 (tttt) REVERT: C 32 TYR cc_start: 0.7464 (m-80) cc_final: 0.7074 (m-80) REVERT: C 46 GLU cc_start: 0.6932 (mp0) cc_final: 0.6189 (mp0) REVERT: C 83 MET cc_start: 0.7353 (mmp) cc_final: 0.7042 (mmp) REVERT: C 87 LYS cc_start: 0.7385 (tmmt) cc_final: 0.7161 (ttpt) REVERT: D 209 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7707 (mmtp) outliers start: 25 outliers final: 19 residues processed: 229 average time/residue: 0.0660 time to fit residues: 20.5399 Evaluate side-chains 234 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 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 1098 GLN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 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 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 19 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN B 169 ASN D 7 GLN D 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130330 restraints weight = 12878.160| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.91 r_work: 0.3553 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7625 Z= 0.152 Angle : 0.603 9.901 10403 Z= 0.304 Chirality : 0.041 0.146 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.199 27.433 1071 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.50 % Allowed : 17.06 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.27), residues: 983 helix: 0.46 (0.29), residues: 326 sheet: -0.54 (0.36), residues: 212 loop : -1.64 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.021 0.001 TYR A1110 PHE 0.010 0.001 PHE A1066 TRP 0.011 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7617) covalent geometry : angle 0.60310 (10387) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.75372 ( 16) hydrogen bonds : bond 0.03570 ( 324) hydrogen bonds : angle 4.76151 ( 945) *********************** 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 260 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7753 (tmtt) cc_final: 0.7449 (tmtt) REVERT: A 309 MET cc_start: 0.7727 (ptm) cc_final: 0.6897 (mtm) REVERT: A 320 ARG cc_start: 0.6360 (tpp80) cc_final: 0.5487 (tpp80) REVERT: A 473 LEU cc_start: 0.8210 (mp) cc_final: 0.7961 (mp) REVERT: A 506 LEU cc_start: 0.7992 (mm) cc_final: 0.7658 (mp) REVERT: A 1004 GLN cc_start: 0.7968 (mp10) cc_final: 0.7444 (mp10) REVERT: A 1009 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 1012 TRP cc_start: 0.8542 (t-100) cc_final: 0.8328 (t-100) REVERT: A 1018 ASN cc_start: 0.7315 (m110) cc_final: 0.7008 (m110) REVERT: A 1033 ASP cc_start: 0.7915 (t0) cc_final: 0.7546 (t0) REVERT: A 1046 GLN cc_start: 0.8274 (mm110) cc_final: 0.8043 (mt0) REVERT: A 1079 ASP cc_start: 0.7135 (m-30) cc_final: 0.6887 (m-30) REVERT: A 543 LEU cc_start: 0.7991 (tp) cc_final: 0.7698 (tt) REVERT: B 50 TRP cc_start: 0.8585 (t60) cc_final: 0.8306 (t60) REVERT: B 80 ASN cc_start: 0.7954 (t0) cc_final: 0.7647 (t0) REVERT: B 157 LYS cc_start: 0.7766 (tttt) cc_final: 0.7456 (tttt) REVERT: C 32 TYR cc_start: 0.7414 (m-80) cc_final: 0.7030 (m-80) REVERT: C 46 GLU cc_start: 0.6860 (mp0) cc_final: 0.6097 (mp0) REVERT: C 83 MET cc_start: 0.7292 (mmp) cc_final: 0.7082 (mmp) outliers start: 34 outliers final: 24 residues processed: 235 average time/residue: 0.0569 time to fit residues: 18.2013 Evaluate side-chains 235 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 609 MET 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 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 ASN 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 = 0.4063 r_free = 0.4063 target = 0.158258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131032 restraints weight = 12621.407| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.88 r_work: 0.3517 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7625 Z= 0.210 Angle : 0.646 9.637 10403 Z= 0.327 Chirality : 0.043 0.146 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.471 28.286 1071 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.56 % Allowed : 17.59 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.27), residues: 983 helix: 0.42 (0.29), residues: 326 sheet: -0.79 (0.34), residues: 230 loop : -1.63 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 19 TYR 0.021 0.002 TYR A1110 PHE 0.013 0.002 PHE A1070 TRP 0.017 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7617) covalent geometry : angle 0.64528 (10387) SS BOND : bond 0.00196 ( 8) SS BOND : angle 0.77978 ( 16) hydrogen bonds : bond 0.03787 ( 324) hydrogen bonds : angle 4.82330 ( 945) *********************** 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 268 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7787 (tmtt) cc_final: 0.7516 (tmtt) REVERT: A 309 MET cc_start: 0.7847 (ptm) cc_final: 0.6921 (mtm) REVERT: A 320 ARG cc_start: 0.6397 (tpp80) cc_final: 0.5524 (tpp80) REVERT: A 382 ASN cc_start: 0.7904 (t0) cc_final: 0.7683 (t0) REVERT: A 443 ASN cc_start: 0.7102 (m-40) cc_final: 0.6592 (t0) REVERT: A 473 LEU cc_start: 0.8202 (mp) cc_final: 0.7934 (mp) REVERT: A 506 LEU cc_start: 0.8037 (mm) cc_final: 0.7709 (mp) REVERT: A 1004 GLN cc_start: 0.8024 (mp10) cc_final: 0.7436 (mp10) REVERT: A 1009 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 1012 TRP cc_start: 0.8616 (t-100) cc_final: 0.8371 (t-100) REVERT: A 1018 ASN cc_start: 0.7389 (m110) cc_final: 0.7143 (m110) REVERT: A 1033 ASP cc_start: 0.7961 (t0) cc_final: 0.7593 (t0) REVERT: A 1079 ASP cc_start: 0.7250 (m-30) cc_final: 0.7048 (m-30) REVERT: B 50 TRP cc_start: 0.8632 (t60) cc_final: 0.8290 (t60) REVERT: B 80 ASN cc_start: 0.7996 (t0) cc_final: 0.7734 (t0) REVERT: B 157 LYS cc_start: 0.7767 (tttt) cc_final: 0.7465 (tttt) REVERT: C 32 TYR cc_start: 0.7444 (m-80) cc_final: 0.7147 (m-80) REVERT: C 46 GLU cc_start: 0.6901 (mp0) cc_final: 0.6131 (mp0) outliers start: 42 outliers final: 33 residues processed: 239 average time/residue: 0.0672 time to fit residues: 21.5626 Evaluate side-chains 252 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 GLU 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 503 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 98 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 ASN A1030 GLN A1046 GLN B 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130778 restraints weight = 12547.744| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.89 r_work: 0.3520 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7625 Z= 0.190 Angle : 0.650 9.970 10403 Z= 0.328 Chirality : 0.042 0.145 1187 Planarity : 0.005 0.066 1315 Dihedral : 4.471 28.167 1071 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.42 % Allowed : 19.58 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.27), residues: 983 helix: 0.46 (0.29), residues: 326 sheet: -0.76 (0.35), residues: 215 loop : -1.63 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1103 TYR 0.035 0.002 TYR D 50 PHE 0.010 0.001 PHE A 490 TRP 0.012 0.001 TRP A 435 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7617) covalent geometry : angle 0.64969 (10387) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.74106 ( 16) hydrogen bonds : bond 0.03592 ( 324) hydrogen bonds : angle 4.77519 ( 945) *********************** 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 259 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7817 (tmtt) cc_final: 0.7554 (tmtt) REVERT: A 309 MET cc_start: 0.7806 (ptm) cc_final: 0.6929 (mtm) REVERT: A 320 ARG cc_start: 0.6435 (tpp80) cc_final: 0.5578 (tpp80) REVERT: A 414 MET cc_start: 0.7510 (mmp) cc_final: 0.7163 (mmm) REVERT: A 443 ASN cc_start: 0.7090 (m-40) cc_final: 0.6573 (t0) REVERT: A 454 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6807 (m) REVERT: A 473 LEU cc_start: 0.8263 (mp) cc_final: 0.7990 (mp) REVERT: A 506 LEU cc_start: 0.8052 (mm) cc_final: 0.7700 (mp) REVERT: A 1004 GLN cc_start: 0.8043 (mp10) cc_final: 0.7419 (mp10) REVERT: A 1009 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 1012 TRP cc_start: 0.8627 (t-100) cc_final: 0.8364 (t-100) REVERT: A 1015 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8048 (mt) REVERT: A 1018 ASN cc_start: 0.7371 (m110) cc_final: 0.7132 (m110) REVERT: A 1033 ASP cc_start: 0.7976 (t0) cc_final: 0.7696 (t0) REVERT: A 1112 GLU cc_start: 0.8082 (tp30) cc_final: 0.7815 (tp30) REVERT: B 50 TRP cc_start: 0.8629 (t60) cc_final: 0.8298 (t60) REVERT: B 80 ASN cc_start: 0.7980 (t0) cc_final: 0.7724 (t0) REVERT: B 157 LYS cc_start: 0.7754 (tttt) cc_final: 0.7440 (tttt) REVERT: C 46 GLU cc_start: 0.6883 (mp0) cc_final: 0.6095 (mp0) REVERT: D 209 LYS cc_start: 0.7870 (mmtp) cc_final: 0.7595 (mttp) outliers start: 41 outliers final: 32 residues processed: 232 average time/residue: 0.0682 time to fit residues: 21.4303 Evaluate side-chains 252 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 THR 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 1072 ILE Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 3 ILE 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 54 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.0270 chunk 88 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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** A1016 ASN A1046 GLN A1108 GLN B 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.160477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133560 restraints weight = 12685.902| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.93 r_work: 0.3563 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7625 Z= 0.113 Angle : 0.614 10.051 10403 Z= 0.307 Chirality : 0.040 0.139 1187 Planarity : 0.005 0.069 1315 Dihedral : 4.261 26.180 1071 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.57 % Allowed : 21.56 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.27), residues: 983 helix: 0.66 (0.30), residues: 326 sheet: -0.42 (0.36), residues: 201 loop : -1.56 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.035 0.001 TYR D 50 PHE 0.008 0.001 PHE A1066 TRP 0.007 0.001 TRP A 620 HIS 0.001 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7617) covalent geometry : angle 0.61362 (10387) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.59785 ( 16) hydrogen bonds : bond 0.03170 ( 324) hydrogen bonds : angle 4.52701 ( 945) *********************** 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 243 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7846 (tmtt) cc_final: 0.7557 (tmtt) REVERT: A 309 MET cc_start: 0.7738 (ptm) cc_final: 0.6885 (mtm) REVERT: A 320 ARG cc_start: 0.6404 (tpp80) cc_final: 0.5550 (tpp80) REVERT: A 414 MET cc_start: 0.7477 (mmp) cc_final: 0.7162 (mmm) REVERT: A 443 ASN cc_start: 0.7024 (m-40) cc_final: 0.6567 (t0) REVERT: A 473 LEU cc_start: 0.8185 (mp) cc_final: 0.7907 (mp) REVERT: A 501 ILE cc_start: 0.7805 (mt) cc_final: 0.7576 (mt) REVERT: A 506 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 1004 GLN cc_start: 0.7983 (mp10) cc_final: 0.7377 (mp10) REVERT: A 1009 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 1012 TRP cc_start: 0.8589 (t-100) cc_final: 0.8300 (t-100) REVERT: A 1015 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8049 (mt) REVERT: A 1018 ASN cc_start: 0.7323 (m110) cc_final: 0.7094 (m110) REVERT: A 1033 ASP cc_start: 0.8025 (t0) cc_final: 0.7687 (t0) REVERT: A 1112 GLU cc_start: 0.8063 (tp30) cc_final: 0.7755 (tp30) REVERT: B 80 ASN cc_start: 0.7923 (t0) cc_final: 0.7640 (t0) REVERT: B 157 LYS cc_start: 0.7714 (tttt) cc_final: 0.7406 (tttt) REVERT: C 6 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5571 (pt0) REVERT: C 46 GLU cc_start: 0.6723 (mp0) cc_final: 0.5958 (mp0) outliers start: 27 outliers final: 23 residues processed: 222 average time/residue: 0.0695 time to fit residues: 20.8326 Evaluate side-chains 240 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP 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 484 VAL 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 609 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 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 76 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 42 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.160520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133643 restraints weight = 12755.414| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.95 r_work: 0.3567 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7625 Z= 0.118 Angle : 0.622 10.502 10403 Z= 0.308 Chirality : 0.041 0.142 1187 Planarity : 0.005 0.075 1315 Dihedral : 4.178 25.726 1071 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.57 % Allowed : 21.83 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.27), residues: 983 helix: 0.77 (0.30), residues: 326 sheet: -0.43 (0.36), residues: 204 loop : -1.61 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.033 0.001 TYR D 50 PHE 0.008 0.001 PHE A 490 TRP 0.010 0.001 TRP A 420 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7617) covalent geometry : angle 0.62181 (10387) SS BOND : bond 0.00185 ( 8) SS BOND : angle 0.57147 ( 16) hydrogen bonds : bond 0.03131 ( 324) hydrogen bonds : angle 4.44790 ( 945) *********************** 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 246 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7851 (tmtt) cc_final: 0.7572 (tmtt) REVERT: A 320 ARG cc_start: 0.6396 (tpp80) cc_final: 0.5551 (tpp80) REVERT: A 414 MET cc_start: 0.7501 (mmp) cc_final: 0.7202 (mmm) REVERT: A 473 LEU cc_start: 0.8204 (mp) cc_final: 0.7943 (mp) REVERT: A 501 ILE cc_start: 0.7865 (mt) cc_final: 0.7629 (mt) REVERT: A 506 LEU cc_start: 0.7969 (mm) cc_final: 0.7672 (mp) REVERT: A 1004 GLN cc_start: 0.8009 (mp10) cc_final: 0.7407 (mp10) REVERT: A 1009 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 1012 TRP cc_start: 0.8591 (t-100) cc_final: 0.8248 (t-100) REVERT: A 1018 ASN cc_start: 0.7333 (m110) cc_final: 0.7126 (m110) REVERT: A 1033 ASP cc_start: 0.7940 (t0) cc_final: 0.7615 (t0) REVERT: B 80 ASN cc_start: 0.7938 (t0) cc_final: 0.7692 (t0) REVERT: B 157 LYS cc_start: 0.7711 (tttt) cc_final: 0.7419 (tttt) REVERT: C 46 GLU cc_start: 0.6742 (mp0) cc_final: 0.5945 (mp0) REVERT: D 70 THR cc_start: 0.8171 (p) cc_final: 0.7944 (p) REVERT: D 209 LYS cc_start: 0.7597 (mttp) cc_final: 0.7187 (mttt) outliers start: 27 outliers final: 27 residues processed: 226 average time/residue: 0.0705 time to fit residues: 21.3817 Evaluate side-chains 242 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 365 VAL Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 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 1106 TYR Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 135 VAL 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 60 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 GLN B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130716 restraints weight = 12451.566| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.88 r_work: 0.3513 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7625 Z= 0.231 Angle : 0.687 9.873 10403 Z= 0.348 Chirality : 0.044 0.153 1187 Planarity : 0.005 0.079 1315 Dihedral : 4.540 27.791 1071 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.37 % Allowed : 21.56 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.27), residues: 983 helix: 0.53 (0.29), residues: 325 sheet: -0.60 (0.34), residues: 220 loop : -1.76 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.031 0.002 TYR D 50 PHE 0.014 0.002 PHE A1070 TRP 0.019 0.002 TRP A 435 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7617) covalent geometry : angle 0.68673 (10387) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.82447 ( 16) hydrogen bonds : bond 0.03734 ( 324) hydrogen bonds : angle 4.75629 ( 945) *********************** 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 259 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7926 (tmtt) cc_final: 0.7701 (tmtt) REVERT: A 320 ARG cc_start: 0.6384 (tpp80) cc_final: 0.5537 (tpp80) REVERT: A 414 MET cc_start: 0.7559 (mmp) cc_final: 0.7249 (mmm) REVERT: A 443 ASN cc_start: 0.7192 (m-40) cc_final: 0.6696 (t0) REVERT: A 454 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.6949 (m) REVERT: A 473 LEU cc_start: 0.8289 (mp) cc_final: 0.8030 (mp) REVERT: A 506 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 1004 GLN cc_start: 0.8068 (mp10) cc_final: 0.7471 (mp10) REVERT: A 1009 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 1012 TRP cc_start: 0.8663 (t-100) cc_final: 0.8388 (t-100) REVERT: A 1018 ASN cc_start: 0.7419 (m110) cc_final: 0.7189 (m110) REVERT: A 1033 ASP cc_start: 0.8116 (t0) cc_final: 0.7801 (t0) REVERT: A 1067 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7837 (ttm170) REVERT: A 1100 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7694 (mmmt) REVERT: B 50 TRP cc_start: 0.8654 (t60) cc_final: 0.8331 (t60) REVERT: B 80 ASN cc_start: 0.8006 (t0) cc_final: 0.7800 (t0) REVERT: B 157 LYS cc_start: 0.7704 (tttt) cc_final: 0.7409 (tttt) REVERT: C 46 GLU cc_start: 0.6930 (mp0) cc_final: 0.6114 (mp0) REVERT: C 62 ASP cc_start: 0.7881 (m-30) cc_final: 0.7659 (m-30) REVERT: C 68 PHE cc_start: 0.7221 (m-80) cc_final: 0.6912 (m-80) REVERT: D 104 THR cc_start: 0.8460 (m) cc_final: 0.8177 (m) REVERT: D 209 LYS cc_start: 0.7651 (mttp) cc_final: 0.7182 (mttp) outliers start: 33 outliers final: 26 residues processed: 235 average time/residue: 0.0684 time to fit residues: 21.6917 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 : 0.213 ------------------------------------------------------------------------------- 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 365 VAL 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 506 LEU Chi-restraints excluded: chain A residue 1005 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 609 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU 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 C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 135 VAL 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 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 93 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: 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 = 0.4072 r_free = 0.4072 target = 0.159347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132605 restraints weight = 12498.963| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.93 r_work: 0.3538 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7625 Z= 0.151 Angle : 0.677 11.892 10403 Z= 0.332 Chirality : 0.043 0.251 1187 Planarity : 0.005 0.079 1315 Dihedral : 4.421 26.880 1071 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.03 % Allowed : 21.69 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.27), residues: 983 helix: 0.57 (0.29), residues: 325 sheet: -0.53 (0.36), residues: 206 loop : -1.63 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 72 TYR 0.035 0.002 TYR D 50 PHE 0.008 0.001 PHE A1066 TRP 0.011 0.001 TRP B 39 HIS 0.002 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7617) covalent geometry : angle 0.67675 (10387) SS BOND : bond 0.00219 ( 8) SS BOND : angle 0.70517 ( 16) hydrogen bonds : bond 0.03419 ( 324) hydrogen bonds : angle 4.68832 ( 945) ********************** 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 259 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7673 (tmtt) REVERT: A 315 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7036 (mt-10) REVERT: A 382 ASN cc_start: 0.7908 (t0) cc_final: 0.7697 (t0) REVERT: A 414 MET cc_start: 0.7483 (mmp) cc_final: 0.7213 (mmm) REVERT: A 443 ASN cc_start: 0.7158 (m-40) cc_final: 0.6661 (t0) REVERT: A 454 VAL cc_start: 0.7243 (OUTLIER) cc_final: 0.6866 (m) REVERT: A 506 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7669 (mp) REVERT: A 1004 GLN cc_start: 0.8055 (mp10) cc_final: 0.7436 (mp10) REVERT: A 1009 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 1012 TRP cc_start: 0.8624 (t-100) cc_final: 0.8323 (t-100) REVERT: A 1015 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 1018 ASN cc_start: 0.7325 (m110) cc_final: 0.7091 (m110) REVERT: A 1033 ASP cc_start: 0.8161 (t0) cc_final: 0.7829 (t0) REVERT: A 1067 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7842 (ttm170) REVERT: B 50 TRP cc_start: 0.8617 (t60) cc_final: 0.8310 (t60) REVERT: B 80 ASN cc_start: 0.7996 (t0) cc_final: 0.7769 (t0) REVERT: B 157 LYS cc_start: 0.7658 (tttt) cc_final: 0.7369 (tttt) REVERT: C 6 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5622 (pt0) REVERT: C 46 GLU cc_start: 0.6807 (mp0) cc_final: 0.6024 (mp0) REVERT: C 62 ASP cc_start: 0.7886 (m-30) cc_final: 0.7671 (m-30) REVERT: C 87 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7182 (tmtt) REVERT: D 209 LYS cc_start: 0.7604 (mttp) cc_final: 0.7120 (mttp) outliers start: 38 outliers final: 29 residues processed: 232 average time/residue: 0.0933 time to fit residues: 28.9279 Evaluate side-chains 253 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 365 VAL 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 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 1106 TYR Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 135 VAL 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 71 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 72 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4071 r_free = 0.4071 target = 0.159058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132377 restraints weight = 12387.698| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.89 r_work: 0.3539 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7625 Z= 0.156 Angle : 0.672 11.538 10403 Z= 0.330 Chirality : 0.042 0.235 1187 Planarity : 0.005 0.076 1315 Dihedral : 4.398 26.549 1071 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.03 % Allowed : 21.83 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.27), residues: 983 helix: 0.54 (0.29), residues: 325 sheet: -0.52 (0.36), residues: 205 loop : -1.66 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.034 0.002 TYR D 50 PHE 0.009 0.001 PHE A1070 TRP 0.011 0.001 TRP B 39 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7617) covalent geometry : angle 0.67230 (10387) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.70245 ( 16) hydrogen bonds : bond 0.03400 ( 324) hydrogen bonds : angle 4.66642 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.00 seconds wall clock time: 27 minutes 17.14 seconds (1637.14 seconds total)