Starting phenix.real_space_refine on Sat Apr 6 06:48:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9o_36112/04_2024/8j9o_36112_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9o_36112/04_2024/8j9o_36112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9o_36112/04_2024/8j9o_36112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9o_36112/04_2024/8j9o_36112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9o_36112/04_2024/8j9o_36112_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9o_36112/04_2024/8j9o_36112_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4758 2.51 5 N 1240 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7441 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3336 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 4 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1633 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 891 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1581 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.39, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 34.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 312 through 344 removed outlier: 3.508A pdb=" N TRP A 326 " --> pdb=" O TRP A 322 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 removed outlier: 3.748A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 431 removed outlier: 4.347A pdb=" N PHE A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.703A pdb=" N GLU A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.710A pdb=" N ILE A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 514 Processing helix chain 'A' and resid 1002 through 1025 removed outlier: 3.873A pdb=" N THR A1014 " --> pdb=" O ASP A1010 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1048 removed outlier: 3.569A pdb=" N VAL A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1041 " --> pdb=" O LYS A1037 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1068 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.549A pdb=" N LEU A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 removed outlier: 3.629A pdb=" N ALA A1094 " --> pdb=" O LYS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 removed outlier: 3.757A pdb=" N THR A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'A' and resid 531 through 556 Proline residue: A 547 - end of helix removed outlier: 4.009A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 574 removed outlier: 4.178A pdb=" N ARG A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 571 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.621A pdb=" N PHE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 608 " --> pdb=" O MET A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 622 removed outlier: 4.092A pdb=" N GLY A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 622 " --> pdb=" O GLY A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 removed outlier: 3.524A pdb=" N PHE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.700A pdb=" N LYS B 68 " --> pdb=" O ASP B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.917A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.678A pdb=" N LYS B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.103A pdb=" N VAL D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 382 removed outlier: 4.184A pdb=" N THR A 392 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.628A pdb=" N ASP A 469 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.531A pdb=" N GLN B 6 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 10 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.508A pdb=" N ALA B 100 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR B 53 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 53 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER B 62 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 55 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 134 through 138 removed outlier: 4.304A pdb=" N GLY B 153 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR B 190 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.559A pdb=" N ASN B 211 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.590A pdb=" N CYS C 22 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.956A pdb=" N ARG C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 40 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 99 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 39 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.582A pdb=" N VAL D 20 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.532A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 91 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.532A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.508A pdb=" N SER D 116 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 139 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 134 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 177 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.601A pdb=" N ALA D 195 " --> pdb=" O LYS D 151 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 3.10 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: 96.63 - 104.12: 92 104.12 - 111.61: 3436 111.61 - 119.10: 2618 119.10 - 126.59: 4105 126.59 - 134.08: 136 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 2.440 nonbonded pdb=" OG SER C 100 " pdb=" OG SER C 107 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 167 " pdb=" OD1 ASN B 211 " model vdw 2.222 2.440 nonbonded pdb=" NE2 GLN D 91 " pdb=" O LEU D 97 " model vdw 2.232 2.520 nonbonded pdb=" OG SER D 66 " pdb=" OG1 THR D 73 " model vdw 2.261 2.440 ... (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 ========== 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.350 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7617 Z= 0.207 Angle : 0.748 10.744 10387 Z= 0.385 Chirality : 0.044 0.184 1187 Planarity : 0.006 0.101 1315 Dihedral : 13.166 88.719 2566 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 983 helix: -0.73 (0.27), residues: 309 sheet: -0.47 (0.36), residues: 204 loop : -1.69 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.003 0.001 HIS B 178 PHE 0.014 0.001 PHE A 561 TYR 0.016 0.001 TYR D 92 ARG 0.002 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.813 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: 0.2013 time to fit residues: 59.8723 Evaluate side-chains 202 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7617 Z= 0.228 Angle : 0.609 8.950 10387 Z= 0.311 Chirality : 0.041 0.138 1187 Planarity : 0.005 0.073 1315 Dihedral : 4.343 29.853 1071 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.12 % Allowed : 11.64 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.26), residues: 983 helix: -0.06 (0.28), residues: 326 sheet: -0.68 (0.34), residues: 237 loop : -1.67 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 569 HIS 0.002 0.001 HIS B 38 PHE 0.016 0.001 PHE A1066 TYR 0.017 0.001 TYR A 306 ARG 0.003 0.000 ARG C 52 *********************** 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 233 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 PHE cc_start: 0.6614 (t80) cc_final: 0.6407 (t80) REVERT: A 294 LYS cc_start: 0.7723 (tmtt) cc_final: 0.7452 (tmtt) REVERT: A 320 ARG cc_start: 0.6091 (tpp80) cc_final: 0.5305 (tpp80) REVERT: A 433 MET cc_start: 0.7464 (ttm) cc_final: 0.7259 (ttt) REVERT: A 443 ASN cc_start: 0.6910 (m-40) cc_final: 0.6650 (t0) REVERT: A 506 LEU cc_start: 0.7892 (mm) cc_final: 0.7635 (mp) REVERT: A 1004 GLN cc_start: 0.7473 (mp10) cc_final: 0.6848 (mp10) REVERT: A 1016 ASN cc_start: 0.6559 (m-40) cc_final: 0.4679 (m110) REVERT: A 1018 ASN cc_start: 0.7245 (m110) cc_final: 0.6870 (m110) REVERT: A 1033 ASP cc_start: 0.7369 (t0) cc_final: 0.7061 (t0) REVERT: A 1079 ASP cc_start: 0.6730 (m-30) cc_final: 0.6519 (m-30) REVERT: A 543 LEU cc_start: 0.7841 (tp) cc_final: 0.7562 (tt) REVERT: B 80 ASN cc_start: 0.7680 (t0) cc_final: 0.7415 (t0) REVERT: B 157 LYS cc_start: 0.7565 (tttt) cc_final: 0.7233 (tttt) REVERT: C 46 GLU cc_start: 0.6216 (mp0) cc_final: 0.5605 (mp0) outliers start: 16 outliers final: 10 residues processed: 220 average time/residue: 0.2020 time to fit residues: 58.8460 Evaluate side-chains 225 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 211 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1085 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7617 Z= 0.238 Angle : 0.604 9.913 10387 Z= 0.304 Chirality : 0.041 0.136 1187 Planarity : 0.005 0.064 1315 Dihedral : 4.308 28.476 1071 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.44 % Allowed : 15.34 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.27), residues: 983 helix: 0.25 (0.29), residues: 327 sheet: -0.79 (0.35), residues: 224 loop : -1.58 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 452 HIS 0.002 0.000 HIS B 38 PHE 0.013 0.001 PHE A1066 TYR 0.021 0.001 TYR C 104 ARG 0.002 0.000 ARG C 52 *********************** 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 256 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 230 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7560 (tmtt) REVERT: A 309 MET cc_start: 0.7330 (ptm) cc_final: 0.6733 (mtm) REVERT: A 506 LEU cc_start: 0.7906 (mm) cc_final: 0.7602 (mp) REVERT: A 513 LEU cc_start: 0.8341 (tp) cc_final: 0.8060 (tt) REVERT: A 1004 GLN cc_start: 0.7467 (mp10) cc_final: 0.6841 (mp10) REVERT: A 1012 TRP cc_start: 0.8354 (t-100) cc_final: 0.8079 (t-100) REVERT: A 1018 ASN cc_start: 0.7153 (m110) cc_final: 0.6872 (m110) REVERT: A 1033 ASP cc_start: 0.7436 (t0) cc_final: 0.7101 (t0) REVERT: A 543 LEU cc_start: 0.7796 (tp) cc_final: 0.7512 (tt) REVERT: B 50 TRP cc_start: 0.8501 (t60) cc_final: 0.7986 (t60) REVERT: B 157 LYS cc_start: 0.7592 (tttt) cc_final: 0.7257 (tttt) REVERT: C 46 GLU cc_start: 0.6175 (mp0) cc_final: 0.5507 (mp0) outliers start: 26 outliers final: 21 residues processed: 237 average time/residue: 0.1996 time to fit residues: 62.9291 Evaluate side-chains 241 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP 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 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 211 ASN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7617 Z= 0.200 Angle : 0.578 9.258 10387 Z= 0.291 Chirality : 0.041 0.140 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.201 28.091 1071 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.23 % Allowed : 17.72 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.27), residues: 983 helix: 0.50 (0.29), residues: 326 sheet: -0.32 (0.36), residues: 212 loop : -1.68 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 420 HIS 0.002 0.000 HIS B 38 PHE 0.010 0.001 PHE A1066 TYR 0.020 0.001 TYR A1110 ARG 0.001 0.000 ARG D 110 *********************** 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 258 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.7751 (tmtt) cc_final: 0.7540 (tmtt) REVERT: A 309 MET cc_start: 0.7390 (ptm) cc_final: 0.6799 (mtm) REVERT: A 414 MET cc_start: 0.7198 (mmp) cc_final: 0.6784 (mmm) REVERT: A 443 ASN cc_start: 0.7017 (m-40) cc_final: 0.6645 (t0) REVERT: A 506 LEU cc_start: 0.7946 (mm) cc_final: 0.7612 (mp) REVERT: A 513 LEU cc_start: 0.8313 (tp) cc_final: 0.8033 (tt) REVERT: A 1004 GLN cc_start: 0.7452 (mp10) cc_final: 0.6829 (mp10) REVERT: A 1009 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 1033 ASP cc_start: 0.7413 (t0) cc_final: 0.7061 (t0) REVERT: A 1046 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7966 (mt0) REVERT: A 1108 GLN cc_start: 0.8192 (tp40) cc_final: 0.7973 (tp-100) REVERT: A 543 LEU cc_start: 0.7801 (tp) cc_final: 0.7517 (tt) REVERT: B 50 TRP cc_start: 0.8480 (t60) cc_final: 0.8181 (t60) REVERT: B 80 ASN cc_start: 0.7529 (t0) cc_final: 0.7244 (t0) REVERT: B 157 LYS cc_start: 0.7581 (tttt) cc_final: 0.7266 (tttt) REVERT: C 46 GLU cc_start: 0.6112 (mp0) cc_final: 0.5410 (mp0) outliers start: 32 outliers final: 25 residues processed: 235 average time/residue: 0.2000 time to fit residues: 62.8582 Evaluate side-chains 242 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1098 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 108 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 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1030 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7617 Z= 0.244 Angle : 0.600 9.723 10387 Z= 0.302 Chirality : 0.041 0.149 1187 Planarity : 0.005 0.063 1315 Dihedral : 4.308 27.981 1071 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.82 % Allowed : 18.78 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 983 helix: 0.53 (0.29), residues: 325 sheet: -0.73 (0.35), residues: 224 loop : -1.62 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 452 HIS 0.002 0.000 HIS B 214 PHE 0.010 0.001 PHE A1066 TYR 0.020 0.001 TYR A1110 ARG 0.002 0.000 ARG D 19 *********************** 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 fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6775 (mtm) REVERT: A 443 ASN cc_start: 0.7058 (m-40) cc_final: 0.6715 (t0) REVERT: A 506 LEU cc_start: 0.7970 (mm) cc_final: 0.7656 (mp) REVERT: A 513 LEU cc_start: 0.8309 (tp) cc_final: 0.8029 (tt) REVERT: A 1004 GLN cc_start: 0.7492 (mp10) cc_final: 0.6850 (mp10) REVERT: A 1009 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7070 (mm-30) REVERT: A 1012 TRP cc_start: 0.8352 (t-100) cc_final: 0.8108 (t-100) REVERT: A 1033 ASP cc_start: 0.7429 (t0) cc_final: 0.7188 (t0) REVERT: A 1046 GLN cc_start: 0.8212 (mm-40) cc_final: 0.8001 (mt0) REVERT: A 1108 GLN cc_start: 0.8182 (tp40) cc_final: 0.7940 (tp-100) REVERT: B 50 TRP cc_start: 0.8515 (t60) cc_final: 0.8199 (t60) REVERT: B 80 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7293 (t0) REVERT: B 157 LYS cc_start: 0.7578 (tttt) cc_final: 0.7259 (tttt) REVERT: C 46 GLU cc_start: 0.6089 (mp0) cc_final: 0.5369 (mp0) REVERT: C 68 PHE cc_start: 0.6899 (m-80) cc_final: 0.6495 (m-80) outliers start: 44 outliers final: 36 residues processed: 236 average time/residue: 0.1945 time to fit residues: 61.1318 Evaluate side-chains 261 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1030 GLN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1072 ILE 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 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 80 ASN 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 C residue 83 MET Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1016 ASN A1018 ASN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7617 Z= 0.280 Angle : 0.632 9.971 10387 Z= 0.318 Chirality : 0.042 0.156 1187 Planarity : 0.005 0.064 1315 Dihedral : 4.429 28.329 1071 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.82 % Allowed : 20.24 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.27), residues: 983 helix: 0.48 (0.29), residues: 325 sheet: -0.73 (0.35), residues: 228 loop : -1.68 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 435 HIS 0.002 0.000 HIS B 214 PHE 0.022 0.002 PHE A 290 TYR 0.020 0.001 TYR A1110 ARG 0.002 0.000 ARG D 62 *********************** 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 267 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6758 (mtm) REVERT: A 365 VAL cc_start: 0.7851 (p) cc_final: 0.7625 (p) REVERT: A 454 VAL cc_start: 0.7206 (OUTLIER) cc_final: 0.6809 (m) REVERT: A 506 LEU cc_start: 0.7988 (mm) cc_final: 0.7686 (mp) REVERT: A 513 LEU cc_start: 0.8325 (tp) cc_final: 0.8037 (tt) REVERT: A 1004 GLN cc_start: 0.7517 (mp10) cc_final: 0.6866 (mp10) REVERT: A 1009 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7061 (mm-30) REVERT: A 1016 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6228 (m-40) REVERT: A 1033 ASP cc_start: 0.7478 (t0) cc_final: 0.7187 (t0) REVERT: A 1108 GLN cc_start: 0.8182 (tp40) cc_final: 0.7948 (tp-100) REVERT: B 80 ASN cc_start: 0.7598 (t0) cc_final: 0.7249 (t0) REVERT: B 157 LYS cc_start: 0.7576 (tttt) cc_final: 0.7258 (tttt) REVERT: C 46 GLU cc_start: 0.6110 (mp0) cc_final: 0.5385 (mp0) REVERT: C 68 PHE cc_start: 0.6944 (m-80) cc_final: 0.6550 (m-80) outliers start: 44 outliers final: 36 residues processed: 236 average time/residue: 0.1996 time to fit residues: 62.5359 Evaluate side-chains 255 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 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 483 ASN 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 1016 ASN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1098 GLN Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1016 ASN A1046 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 80 ASN B 169 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7617 Z= 0.246 Angle : 0.626 10.304 10387 Z= 0.313 Chirality : 0.041 0.155 1187 Planarity : 0.005 0.066 1315 Dihedral : 4.425 28.040 1071 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.95 % Allowed : 21.16 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 983 helix: 0.53 (0.29), residues: 325 sheet: -0.56 (0.35), residues: 225 loop : -1.67 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1012 HIS 0.002 0.000 HIS B 214 PHE 0.010 0.001 PHE A 406 TYR 0.023 0.001 TYR C 104 ARG 0.005 0.000 ARG C 27 *********************** 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 265 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6733 (mtm) REVERT: A 454 VAL cc_start: 0.7251 (OUTLIER) cc_final: 0.7027 (p) REVERT: A 506 LEU cc_start: 0.7997 (mm) cc_final: 0.7669 (mp) REVERT: A 513 LEU cc_start: 0.8287 (tp) cc_final: 0.8021 (tt) REVERT: A 1004 GLN cc_start: 0.7481 (mp10) cc_final: 0.6834 (mp10) REVERT: A 1009 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 1015 LEU cc_start: 0.8483 (mt) cc_final: 0.7990 (mt) REVERT: A 1033 ASP cc_start: 0.7457 (t0) cc_final: 0.7155 (t0) REVERT: A 1108 GLN cc_start: 0.8166 (tp40) cc_final: 0.7930 (tp-100) REVERT: B 80 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7227 (t0) REVERT: B 157 LYS cc_start: 0.7560 (tttt) cc_final: 0.7241 (tttt) REVERT: C 46 GLU cc_start: 0.6079 (mp0) cc_final: 0.5301 (mp0) REVERT: C 68 PHE cc_start: 0.6923 (m-80) cc_final: 0.6521 (m-80) outliers start: 45 outliers final: 38 residues processed: 234 average time/residue: 0.2043 time to fit residues: 63.2685 Evaluate side-chains 262 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 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 483 ASN 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 1016 ASN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1072 ILE 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 14 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 108 ILE 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 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1016 ASN A1046 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 169 ASN D 7 GLN D 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7617 Z= 0.226 Angle : 0.626 10.730 10387 Z= 0.312 Chirality : 0.041 0.143 1187 Planarity : 0.005 0.065 1315 Dihedral : 4.413 27.678 1071 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.08 % Allowed : 21.30 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.27), residues: 983 helix: 0.54 (0.29), residues: 325 sheet: -0.52 (0.35), residues: 225 loop : -1.67 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1012 HIS 0.002 0.000 HIS B 214 PHE 0.009 0.001 PHE A1066 TYR 0.022 0.001 TYR C 104 ARG 0.005 0.000 ARG A1103 *********************** 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 273 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6752 (mtm) REVERT: A 315 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6718 (mt-10) REVERT: A 320 ARG cc_start: 0.6126 (tpp80) cc_final: 0.5247 (tpp80) REVERT: A 365 VAL cc_start: 0.7814 (p) cc_final: 0.7586 (p) REVERT: A 454 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.6876 (m) REVERT: A 506 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7648 (mp) REVERT: A 513 LEU cc_start: 0.8320 (tp) cc_final: 0.8054 (tt) REVERT: A 1004 GLN cc_start: 0.7494 (mp10) cc_final: 0.6855 (mp10) REVERT: A 1009 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 1033 ASP cc_start: 0.7464 (t0) cc_final: 0.7154 (t0) REVERT: A 1099 LEU cc_start: 0.8264 (mp) cc_final: 0.8046 (mp) REVERT: A 1108 GLN cc_start: 0.8189 (tp40) cc_final: 0.7945 (tp-100) REVERT: B 80 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7234 (t0) REVERT: B 157 LYS cc_start: 0.7550 (tttt) cc_final: 0.7238 (tttt) REVERT: C 68 PHE cc_start: 0.6925 (m-80) cc_final: 0.6530 (m-80) outliers start: 46 outliers final: 39 residues processed: 241 average time/residue: 0.2067 time to fit residues: 66.2313 Evaluate side-chains 269 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 395 GLN 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 483 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1016 ASN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1098 GLN Chi-restraints excluded: chain A residue 1106 TYR 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 80 ASN Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 108 ILE 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 88 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1016 ASN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN C 65 GLN D 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7617 Z= 0.208 Angle : 0.633 10.485 10387 Z= 0.313 Chirality : 0.041 0.147 1187 Planarity : 0.005 0.067 1315 Dihedral : 4.397 29.154 1071 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.82 % Allowed : 21.83 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.27), residues: 983 helix: 0.59 (0.29), residues: 325 sheet: -0.51 (0.35), residues: 225 loop : -1.67 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1012 HIS 0.003 0.001 HIS B 214 PHE 0.009 0.001 PHE A1066 TYR 0.020 0.001 TYR C 104 ARG 0.005 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6739 (mtm) REVERT: A 315 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6724 (mt-10) REVERT: A 320 ARG cc_start: 0.6125 (tpp80) cc_final: 0.5254 (tpp80) REVERT: A 365 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7584 (p) REVERT: A 454 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6869 (m) REVERT: A 506 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 513 LEU cc_start: 0.8324 (tp) cc_final: 0.8051 (tt) REVERT: A 1004 GLN cc_start: 0.7499 (mp10) cc_final: 0.6865 (mp10) REVERT: A 1033 ASP cc_start: 0.7447 (t0) cc_final: 0.7144 (t0) REVERT: A 1108 GLN cc_start: 0.8182 (tp40) cc_final: 0.7937 (tp-100) REVERT: B 80 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7359 (t0) REVERT: B 157 LYS cc_start: 0.7527 (tttt) cc_final: 0.7220 (tttt) REVERT: C 68 PHE cc_start: 0.6917 (m-80) cc_final: 0.6516 (m-80) outliers start: 44 outliers final: 38 residues processed: 237 average time/residue: 0.1928 time to fit residues: 60.3861 Evaluate side-chains 265 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 222 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 444 SER 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 483 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1016 ASN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1072 ILE 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 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 99 CYS 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 173 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 108 ILE 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 44 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1030 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN D 7 GLN D 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7617 Z= 0.208 Angle : 0.645 11.925 10387 Z= 0.316 Chirality : 0.042 0.166 1187 Planarity : 0.005 0.069 1315 Dihedral : 4.382 30.924 1071 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.82 % Allowed : 21.69 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 983 helix: 0.62 (0.29), residues: 325 sheet: -0.50 (0.35), residues: 225 loop : -1.66 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1012 HIS 0.003 0.001 HIS B 214 PHE 0.008 0.001 PHE A1066 TYR 0.021 0.001 TYR C 104 ARG 0.005 0.000 ARG C 27 ********************** 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 267 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6741 (mtm) REVERT: A 315 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6727 (mt-10) REVERT: A 320 ARG cc_start: 0.6053 (tpp80) cc_final: 0.5181 (tpp80) REVERT: A 365 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 506 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 513 LEU cc_start: 0.8315 (tp) cc_final: 0.8047 (tt) REVERT: A 1004 GLN cc_start: 0.7492 (mp10) cc_final: 0.6856 (mp10) REVERT: A 1033 ASP cc_start: 0.7531 (t0) cc_final: 0.7246 (t0) REVERT: A 1108 GLN cc_start: 0.8187 (tp40) cc_final: 0.7931 (tp-100) REVERT: B 80 ASN cc_start: 0.7534 (t0) cc_final: 0.7193 (t0) REVERT: B 157 LYS cc_start: 0.7522 (tttt) cc_final: 0.7213 (tttt) REVERT: C 46 GLU cc_start: 0.5975 (mp0) cc_final: 0.5304 (mp0) REVERT: C 68 PHE cc_start: 0.6932 (m-80) cc_final: 0.6534 (m-80) outliers start: 44 outliers final: 39 residues processed: 236 average time/residue: 0.1998 time to fit residues: 62.8230 Evaluate side-chains 260 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 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 444 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1016 ASN Chi-restraints excluded: chain A residue 1030 GLN Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1072 ILE 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 14 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 99 CYS 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 173 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 108 ILE 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 72 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1030 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 169 ASN D 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.156418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129731 restraints weight = 12473.072| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.90 r_work: 0.3548 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7617 Z= 0.170 Angle : 0.624 10.221 10387 Z= 0.308 Chirality : 0.041 0.146 1187 Planarity : 0.005 0.069 1315 Dihedral : 4.324 31.536 1071 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.29 % Allowed : 22.22 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 983 helix: 0.69 (0.30), residues: 325 sheet: -0.42 (0.35), residues: 224 loop : -1.64 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1012 HIS 0.003 0.001 HIS B 214 PHE 0.008 0.001 PHE A 412 TYR 0.021 0.001 TYR C 104 ARG 0.005 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.74 seconds wall clock time: 40 minutes 24.23 seconds (2424.23 seconds total)