Starting phenix.real_space_refine on Wed Mar 12 21:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9x_27967/03_2025/8e9x_27967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9x_27967/03_2025/8e9x_27967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e9x_27967/03_2025/8e9x_27967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9x_27967/03_2025/8e9x_27967.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9x_27967/03_2025/8e9x_27967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9x_27967/03_2025/8e9x_27967.cif" } resolution = 2.7 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= 0.022 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 61 5.16 5 C 5364 2.51 5 N 1401 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8380 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2124 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1666 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2485 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'WEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.63 Number of scatterers: 8380 At special positions: 0 Unit cell: (91.52, 117.04, 128.48, 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 61 16.00 O 1554 8.00 N 1401 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 429 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 2.05 Conformation dependent library (CDL) restraints added in 912.5 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 28 through 60 removed outlier: 3.652A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.611A pdb=" N PHE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 removed outlier: 3.880A pdb=" N THR A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 136 removed outlier: 4.162A pdb=" N ASN A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 170 removed outlier: 3.616A pdb=" N TRP A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.854A pdb=" N LEU A 190 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 191 " --> pdb=" O GLN A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 204 through 221 removed outlier: 3.561A pdb=" N MET A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 4.038A pdb=" N LYS A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.749A pdb=" N LEU A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.530A pdb=" N SER A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.587A pdb=" N ARG A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 removed outlier: 3.994A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.906A pdb=" N ILE B 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.474A pdb=" N ILE B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS B 95 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 127 removed outlier: 4.168A pdb=" N HIS B 116 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.600A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 removed outlier: 3.670A pdb=" N ALA B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 222 removed outlier: 4.058A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.558A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.551A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.628A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.533A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.842A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.786A pdb=" N LYS B 51 " --> pdb=" O HIS B 70 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 31 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE B 81 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 33 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS B 32 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE B 104 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 34 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS B 106 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 36 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP B 108 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.600A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.714A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.373A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.820A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.586A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.743A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.540A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.505A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.505A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.406A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1176 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: 2.49 Time building geometry restraints manager: 2.35 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: 2673 1.34 - 1.46: 2103 1.46 - 1.58: 3703 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 8565 Sorted by residual: bond pdb=" C01 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.455 1.286 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C06 WEC A 501 " pdb=" N07 WEC A 501 " ideal model delta sigma weight residual 1.292 1.452 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C06 WEC A 501 " pdb=" N05 WEC A 501 " ideal model delta sigma weight residual 1.373 1.498 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C03 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.461 1.371 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C22 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.459 1.372 0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 8560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11436 1.71 - 3.41: 193 3.41 - 5.12: 30 5.12 - 6.82: 7 6.82 - 8.53: 4 Bond angle restraints: 11670 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 111.33 117.20 -5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" C TYR A 439 " pdb=" CA TYR A 439 " pdb=" CB TYR A 439 " ideal model delta sigma weight residual 110.56 102.09 8.47 1.83e+00 2.99e-01 2.14e+01 angle pdb=" N ASN B 202 " pdb=" CA ASN B 202 " pdb=" C ASN B 202 " ideal model delta sigma weight residual 114.12 108.45 5.67 1.39e+00 5.18e-01 1.66e+01 angle pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" O ARG E 179 " ideal model delta sigma weight residual 120.98 116.91 4.07 1.24e+00 6.50e-01 1.08e+01 angle pdb=" C ARG A 178 " pdb=" CA ARG A 178 " pdb=" CB ARG A 178 " ideal model delta sigma weight residual 111.78 104.97 6.81 2.20e+00 2.07e-01 9.57e+00 ... (remaining 11665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 4503 15.12 - 30.24: 400 30.24 - 45.37: 82 45.37 - 60.49: 19 60.49 - 75.61: 6 Dihedral angle restraints: 5010 sinusoidal: 1791 harmonic: 3219 Sorted by residual: dihedral pdb=" CA THR E 160 " pdb=" C THR E 160 " pdb=" N TYR E 161 " pdb=" CA TYR E 161 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA CYS A 426 " pdb=" C CYS A 426 " pdb=" N GLN A 427 " pdb=" CA GLN A 427 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -117.07 31.07 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1135 0.054 - 0.108: 189 0.108 - 0.161: 31 0.161 - 0.215: 6 0.215 - 0.269: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA LEU A 52 " pdb=" N LEU A 52 " pdb=" C LEU A 52 " pdb=" CB LEU A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TRP A 440 " pdb=" N TRP A 440 " pdb=" C TRP A 440 " pdb=" CB TRP A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1359 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C ARG E 179 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG E 179 " 0.021 2.00e-02 2.50e+03 pdb=" N MET E 180 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 202 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C ASN B 202 " 0.024 2.00e-02 2.50e+03 pdb=" O ASN B 202 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA B 203 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 153 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 154 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " 0.019 5.00e-02 4.00e+02 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 567 2.74 - 3.28: 8267 3.28 - 3.82: 13795 3.82 - 4.36: 16888 4.36 - 4.90: 29210 Nonbonded interactions: 68727 Sorted by model distance: nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 88 " pdb=" OD2 ASP C 186 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.271 3.040 nonbonded pdb=" ND2 ASN C 340 " pdb=" OD1 ASN D 59 " model vdw 2.319 3.120 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.328 3.040 ... (remaining 68722 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: 1.600 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.040 Find NCS groups from input model: 0.080 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.005 0.169 8565 Z= 0.293 Angle : 0.553 8.530 11670 Z= 0.312 Chirality : 0.044 0.269 1362 Planarity : 0.003 0.034 1470 Dihedral : 12.406 75.609 2925 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.15 (0.26), residues: 1093 helix: 0.51 (0.28), residues: 359 sheet: 0.59 (0.31), residues: 286 loop : -1.00 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.023 0.001 TYR E 178 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.897 Fit side-chains REVERT: A 410 ILE cc_start: 0.7951 (mm) cc_final: 0.7667 (mm) REVERT: B 29 LYS cc_start: 0.7759 (mppt) cc_final: 0.7504 (mppt) REVERT: B 81 PHE cc_start: 0.8308 (m-80) cc_final: 0.7896 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.8035 time to fit residues: 166.0381 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 128 ASN B 202 ASN B 217 ASN C 88 ASN C 110 ASN C 259 GLN C 293 ASN E 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110057 restraints weight = 11794.116| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.73 r_work: 0.3343 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8565 Z= 0.256 Angle : 0.561 7.630 11670 Z= 0.294 Chirality : 0.043 0.173 1362 Planarity : 0.004 0.039 1470 Dihedral : 4.401 29.240 1200 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.72 % Allowed : 10.56 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.47 (0.26), residues: 1093 helix: 1.38 (0.28), residues: 355 sheet: 0.74 (0.31), residues: 282 loop : -0.79 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE C 151 TYR 0.018 0.002 TYR A 92 ARG 0.008 0.001 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 439 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: B 29 LYS cc_start: 0.8212 (mppt) cc_final: 0.7874 (mppt) REVERT: B 217 ASN cc_start: 0.7957 (m-40) cc_final: 0.7748 (m110) REVERT: C 153 ASP cc_start: 0.7742 (p0) cc_final: 0.7533 (p0) outliers start: 15 outliers final: 5 residues processed: 187 average time/residue: 0.8118 time to fit residues: 166.0010 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 0.0770 chunk 19 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 218 ASN C 88 ASN C 110 ASN C 239 ASN C 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111032 restraints weight = 11937.973| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.76 r_work: 0.3357 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.003 0.024 8565 Z= 0.169 Angle : 0.494 7.313 11670 Z= 0.259 Chirality : 0.041 0.139 1362 Planarity : 0.003 0.040 1470 Dihedral : 4.136 25.308 1200 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 12.28 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.72 (0.26), residues: 1093 helix: 1.87 (0.29), residues: 355 sheet: 0.77 (0.31), residues: 270 loop : -0.78 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.013 0.001 PHE C 292 TYR 0.013 0.001 TYR E 178 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 439 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 29 LYS cc_start: 0.8188 (mppt) cc_final: 0.7906 (mppt) REVERT: B 217 ASN cc_start: 0.7965 (m-40) cc_final: 0.7746 (m110) outliers start: 26 outliers final: 12 residues processed: 189 average time/residue: 0.8265 time to fit residues: 170.9682 Evaluate side-chains 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN C 88 ASN C 110 ASN C 259 GLN C 293 ASN E 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110443 restraints weight = 11839.022| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.75 r_work: 0.3350 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8565 Z= 0.199 Angle : 0.504 8.155 11670 Z= 0.263 Chirality : 0.041 0.139 1362 Planarity : 0.003 0.040 1470 Dihedral : 4.194 24.665 1200 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.33 % Allowed : 13.43 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1093 helix: 1.99 (0.29), residues: 350 sheet: 0.74 (0.31), residues: 282 loop : -0.81 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR A 92 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5988 (ppp) cc_final: 0.5685 (ppp) REVERT: A 208 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7845 (t) REVERT: A 439 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: B 217 ASN cc_start: 0.7953 (m-40) cc_final: 0.7752 (m110) outliers start: 29 outliers final: 13 residues processed: 180 average time/residue: 0.9629 time to fit residues: 188.7285 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN C 259 GLN C 293 ASN E 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110545 restraints weight = 11752.474| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.75 r_work: 0.3351 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8565 Z= 0.192 Angle : 0.492 7.426 11670 Z= 0.258 Chirality : 0.041 0.174 1362 Planarity : 0.003 0.038 1470 Dihedral : 4.172 23.721 1200 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.10 % Allowed : 14.58 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1093 helix: 2.06 (0.29), residues: 350 sheet: 0.70 (0.31), residues: 271 loop : -0.78 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.679 Fit side-chains REVERT: A 32 MET cc_start: 0.6007 (ppp) cc_final: 0.5658 (ppp) REVERT: A 208 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7837 (t) REVERT: A 439 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 217 ASN cc_start: 0.7957 (m-40) cc_final: 0.7757 (m110) outliers start: 27 outliers final: 17 residues processed: 182 average time/residue: 0.9145 time to fit residues: 183.5992 Evaluate side-chains 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS B 218 ASN C 88 ASN C 259 GLN C 293 ASN E 82 GLN E 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109365 restraints weight = 11726.369| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.74 r_work: 0.3331 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8565 Z= 0.247 Angle : 0.518 7.529 11670 Z= 0.271 Chirality : 0.042 0.149 1362 Planarity : 0.003 0.037 1470 Dihedral : 4.364 34.098 1200 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.44 % Allowed : 15.04 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1093 helix: 2.06 (0.28), residues: 349 sheet: 0.72 (0.31), residues: 282 loop : -0.87 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.002 PHE A 189 TYR 0.015 0.001 TYR A 92 ARG 0.010 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.985 Fit side-chains REVERT: A 32 MET cc_start: 0.5973 (ppp) cc_final: 0.5649 (ppp) REVERT: A 208 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7864 (t) REVERT: A 439 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: B 217 ASN cc_start: 0.7980 (m-40) cc_final: 0.7763 (m110) outliers start: 30 outliers final: 18 residues processed: 181 average time/residue: 1.0195 time to fit residues: 201.6369 Evaluate side-chains 197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN C 239 ASN C 259 GLN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109203 restraints weight = 11818.593| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.75 r_work: 0.3329 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8565 Z= 0.244 Angle : 0.518 7.494 11670 Z= 0.271 Chirality : 0.042 0.142 1362 Planarity : 0.003 0.035 1470 Dihedral : 4.379 34.457 1200 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.99 % Allowed : 16.07 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1093 helix: 2.07 (0.28), residues: 349 sheet: 0.66 (0.30), residues: 282 loop : -0.87 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR A 92 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.858 Fit side-chains REVERT: A 32 MET cc_start: 0.6033 (ppp) cc_final: 0.5651 (ppp) REVERT: A 208 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 439 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: B 217 ASN cc_start: 0.7961 (m-40) cc_final: 0.7741 (m110) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.8058 time to fit residues: 160.7317 Evaluate side-chains 194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN C 293 ASN C 340 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109835 restraints weight = 11865.247| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.75 r_work: 0.3339 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8565 Z= 0.206 Angle : 0.503 7.443 11670 Z= 0.264 Chirality : 0.041 0.137 1362 Planarity : 0.003 0.037 1470 Dihedral : 4.280 29.484 1200 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.10 % Allowed : 15.84 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.77 (0.26), residues: 1093 helix: 2.12 (0.28), residues: 350 sheet: 0.62 (0.31), residues: 271 loop : -0.80 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.250 Fit side-chains REVERT: A 32 MET cc_start: 0.6017 (ppp) cc_final: 0.5639 (ppp) REVERT: A 208 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 439 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 122 PHE cc_start: 0.7930 (t80) cc_final: 0.7329 (t80) REVERT: B 138 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8405 (tp) REVERT: B 217 ASN cc_start: 0.7965 (m-40) cc_final: 0.7745 (m110) outliers start: 27 outliers final: 18 residues processed: 180 average time/residue: 0.7608 time to fit residues: 150.3046 Evaluate side-chains 193 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.4980 chunk 23 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 93 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 293 ASN C 340 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110778 restraints weight = 12063.125| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.77 r_work: 0.3354 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8565 Z= 0.171 Angle : 0.487 7.398 11670 Z= 0.256 Chirality : 0.041 0.136 1362 Planarity : 0.003 0.035 1470 Dihedral : 4.159 25.177 1200 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.53 % Allowed : 17.11 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1093 helix: 2.23 (0.28), residues: 350 sheet: 0.64 (0.31), residues: 271 loop : -0.76 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.873 Fit side-chains REVERT: A 32 MET cc_start: 0.6036 (ppp) cc_final: 0.5667 (ppp) REVERT: A 208 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7863 (t) REVERT: A 439 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: B 122 PHE cc_start: 0.7918 (t80) cc_final: 0.7331 (t80) REVERT: B 138 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8417 (tp) REVERT: B 217 ASN cc_start: 0.7945 (m-40) cc_final: 0.7721 (m110) outliers start: 22 outliers final: 15 residues processed: 181 average time/residue: 0.8219 time to fit residues: 163.4743 Evaluate side-chains 193 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN C 259 GLN C 293 ASN C 340 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109466 restraints weight = 11775.227| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.75 r_work: 0.3333 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8565 Z= 0.246 Angle : 0.525 7.507 11670 Z= 0.276 Chirality : 0.042 0.142 1362 Planarity : 0.003 0.037 1470 Dihedral : 4.300 22.541 1200 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 16.88 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1093 helix: 2.13 (0.28), residues: 350 sheet: 0.54 (0.31), residues: 273 loop : -0.76 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR A 92 ARG 0.009 0.000 ARG C 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.178 Fit side-chains REVERT: A 32 MET cc_start: 0.6015 (ppp) cc_final: 0.5638 (ppp) REVERT: A 208 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7876 (t) REVERT: A 439 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: B 122 PHE cc_start: 0.7942 (t80) cc_final: 0.7263 (t80) REVERT: B 217 ASN cc_start: 0.7960 (m-40) cc_final: 0.7737 (m110) outliers start: 23 outliers final: 19 residues processed: 179 average time/residue: 1.1435 time to fit residues: 225.1818 Evaluate side-chains 194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 0.0000 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN C 259 GLN C 293 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110880 restraints weight = 12017.397| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.77 r_work: 0.3356 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8565 Z= 0.176 Angle : 0.493 7.394 11670 Z= 0.259 Chirality : 0.041 0.136 1362 Planarity : 0.003 0.035 1470 Dihedral : 4.138 23.425 1200 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.41 % Allowed : 17.91 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.83 (0.26), residues: 1093 helix: 2.21 (0.28), residues: 351 sheet: 0.55 (0.31), residues: 273 loop : -0.73 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6753.42 seconds wall clock time: 119 minutes 51.34 seconds (7191.34 seconds total)