Starting phenix.real_space_refine on Sat Jun 7 06:19:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kdg_62275/06_2025/9kdg_62275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kdg_62275/06_2025/9kdg_62275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kdg_62275/06_2025/9kdg_62275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kdg_62275/06_2025/9kdg_62275.map" model { file = "/net/cci-nas-00/data/ceres_data/9kdg_62275/06_2025/9kdg_62275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kdg_62275/06_2025/9kdg_62275.cif" } resolution = 3.33 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= 0.005 sd= 0.234 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1431 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Fe 1 7.16 5 Zn 1 6.06 5 S 51 5.16 5 C 4725 2.51 5 N 1197 2.21 5 O 1313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7292 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6411 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 767} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 4, ' FE': 1, ' ZN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.95, per 1000 atoms: 0.68 Number of scatterers: 7292 At special positions: 0 Unit cell: (65.072, 95.284, 146.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 Ca 4 19.99 S 51 16.00 O 1313 8.00 N 1197 7.00 C 4725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 505 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1706 " pdb="ZN ZN A1706 " - pdb=" ND1 HIS A1266 " pdb="ZN ZN A1706 " - pdb=" NE2 HIS A1184 " 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 58.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 91 through 129 removed outlier: 4.319A pdb=" N GLU A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 165 removed outlier: 3.964A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.616A pdb=" N LEU A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 removed outlier: 3.583A pdb=" N CYS A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 204 removed outlier: 3.628A pdb=" N VAL A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.698A pdb=" N ALA A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.703A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 282 through 302 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.555A pdb=" N ARG A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.519A pdb=" N ASP A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.585A pdb=" N GLN A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.679A pdb=" N LYS A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.507A pdb=" N MET A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.579A pdb=" N VAL A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 464 through 496 removed outlier: 4.450A pdb=" N VAL A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.571A pdb=" N ARG A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 525 removed outlier: 3.846A pdb=" N LEU A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 525 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1037 Processing helix chain 'A' and resid 1042 through 1059 removed outlier: 3.732A pdb=" N ILE A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1091 removed outlier: 3.599A pdb=" N LYS A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A1088 " --> pdb=" O MET A1084 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1125 Processing helix chain 'A' and resid 1138 through 1145 removed outlier: 3.656A pdb=" N TYR A1144 " --> pdb=" O HIS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1156 through 1169 removed outlier: 3.903A pdb=" N TYR A1160 " --> pdb=" O SER A1156 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.737A pdb=" N ARG A1198 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 Processing helix chain 'A' and resid 1246 through 1257 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1328 through 1332 removed outlier: 3.520A pdb=" N MET A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1355 Proline residue: A1340 - end of helix Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 59 through 68 removed outlier: 3.504A pdb=" N GLN F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 removed outlier: 3.574A pdb=" N ASP A 241 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 256 " --> pdb=" O ASP A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA3, first strand: chain 'A' and resid 1063 through 1066 removed outlier: 5.985A pdb=" N LEU A1064 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A1289 " --> pdb=" O ARG A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1129 through 1131 removed outlier: 3.505A pdb=" N GLU A1310 " --> pdb=" O VAL A1313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1219 through 1220 removed outlier: 6.577A pdb=" N ASP A1219 " --> pdb=" O TYR A1245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 11 removed outlier: 3.503A pdb=" N GLU F 6 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG F 74 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL F 26 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU F 109 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR F 24 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU F 33 " --> pdb=" O LYS F 38 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS F 38 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 11 removed outlier: 3.503A pdb=" N GLU F 6 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG F 74 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL F 26 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU F 109 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR F 24 " --> pdb=" O LEU F 109 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1119 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: 2.29 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2309 1.35 - 1.46: 1717 1.46 - 1.58: 3353 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 7453 Sorted by residual: bond pdb=" C9 FK5 F1201 " pdb=" O4 FK5 F1201 " ideal model delta sigma weight residual 1.206 1.407 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C1 FK5 F1201 " pdb=" O2 FK5 F1201 " ideal model delta sigma weight residual 1.211 1.409 -0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" C22 FK5 F1201 " pdb=" O9 FK5 F1201 " ideal model delta sigma weight residual 1.215 1.405 -0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" C8 FK5 F1201 " pdb=" O3 FK5 F1201 " ideal model delta sigma weight residual 1.232 1.408 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C8 FK5 F1201 " pdb=" C9 FK5 F1201 " ideal model delta sigma weight residual 1.537 1.392 0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 7448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9893 1.94 - 3.89: 152 3.89 - 5.83: 39 5.83 - 7.77: 8 7.77 - 9.72: 3 Bond angle restraints: 10095 Sorted by residual: angle pdb=" C LYS F 47 " pdb=" N PRO F 48 " pdb=" CA PRO F 48 " ideal model delta sigma weight residual 120.98 113.58 7.40 1.07e+00 8.73e-01 4.78e+01 angle pdb=" C ALA A 233 " pdb=" N VAL A 234 " pdb=" CA VAL A 234 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" N VAL A1299 " pdb=" CA VAL A1299 " pdb=" C VAL A1299 " ideal model delta sigma weight residual 113.71 109.46 4.25 9.50e-01 1.11e+00 2.00e+01 angle pdb=" N THR A 244 " pdb=" CA THR A 244 " pdb=" C THR A 244 " ideal model delta sigma weight residual 111.28 116.14 -4.86 1.35e+00 5.49e-01 1.30e+01 angle pdb=" N HIS A1266 " pdb=" CA HIS A1266 " pdb=" CB HIS A1266 " ideal model delta sigma weight residual 114.27 108.57 5.70 1.64e+00 3.72e-01 1.21e+01 ... (remaining 10090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 4463 35.21 - 70.41: 58 70.41 - 105.62: 14 105.62 - 140.83: 0 140.83 - 176.03: 4 Dihedral angle restraints: 4539 sinusoidal: 1895 harmonic: 2644 Sorted by residual: dihedral pdb=" CB CYS A 174 " pdb=" SG CYS A 174 " pdb=" SG CYS A 255 " pdb=" CB CYS A 255 " ideal model delta sinusoidal sigma weight residual -86.00 -167.09 81.09 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 505 " pdb=" CB CYS A 505 " ideal model delta sinusoidal sigma weight residual 93.00 137.75 -44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" O5 FK5 F1201 " pdb=" C14 FK5 F1201 " pdb=" C15 FK5 F1201 " pdb=" O8 FK5 F1201 " ideal model delta sinusoidal sigma weight residual -11.37 164.66 -176.03 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 852 0.044 - 0.087: 224 0.087 - 0.131: 53 0.131 - 0.175: 5 0.175 - 0.219: 5 Chirality restraints: 1139 Sorted by residual: chirality pdb=" C2 FK5 F1201 " pdb=" C1 FK5 F1201 " pdb=" C3 FK5 F1201 " pdb=" N7 FK5 F1201 " both_signs ideal model delta sigma weight residual False 2.33 2.55 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA THR A 244 " pdb=" N THR A 244 " pdb=" C THR A 244 " pdb=" CB THR A 244 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C10 FK5 F1201 " pdb=" C11 FK5 F1201 " pdb=" C9 FK5 F1201 " pdb=" O5 FK5 F1201 " both_signs ideal model delta sigma weight residual False 2.69 2.48 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1136 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 FK5 F1201 " -0.071 2.00e-02 2.50e+03 7.92e-02 7.84e+01 pdb=" C19 FK5 F1201 " 0.022 2.00e-02 2.50e+03 pdb=" C20 FK5 F1201 " 0.126 2.00e-02 2.50e+03 pdb=" C21 FK5 F1201 " -0.098 2.00e-02 2.50e+03 pdb=" C37 FK5 F1201 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 FK5 F1201 " -0.046 2.00e-02 2.50e+03 4.37e-02 2.87e+01 pdb=" C6 FK5 F1201 " 0.057 2.00e-02 2.50e+03 pdb=" C8 FK5 F1201 " -0.012 2.00e-02 2.50e+03 pdb=" C9 FK5 F1201 " -0.047 2.00e-02 2.50e+03 pdb=" N7 FK5 F1201 " -0.013 2.00e-02 2.50e+03 pdb=" O3 FK5 F1201 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 FK5 F1201 " -0.039 2.00e-02 2.50e+03 4.15e-02 2.15e+01 pdb=" C27 FK5 F1201 " 0.015 2.00e-02 2.50e+03 pdb=" C28 FK5 F1201 " 0.063 2.00e-02 2.50e+03 pdb=" C29 FK5 F1201 " -0.052 2.00e-02 2.50e+03 pdb=" C42 FK5 F1201 " 0.012 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 64 2.61 - 3.18: 6380 3.18 - 3.75: 11026 3.75 - 4.33: 15647 4.33 - 4.90: 25654 Nonbonded interactions: 58771 Sorted by model distance: nonbonded pdb=" OD2 ASP A1103 " pdb="ZN ZN A1706 " model vdw 2.035 2.230 nonbonded pdb=" OD2 ASP A1103 " pdb="FE FE A1705 " model vdw 2.036 2.260 nonbonded pdb=" NE2 HIS A1077 " pdb="FE FE A1705 " model vdw 2.039 2.340 nonbonded pdb=" OH TYR F 85 " pdb=" O3 FK5 F1201 " model vdw 2.070 3.040 nonbonded pdb=" OG1 THR A1193 " pdb=" OD1 ASP A1195 " model vdw 2.166 3.040 ... (remaining 58766 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.760 Find NCS groups from input model: 0.090 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 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 : 0.007 0.201 7458 Z= 0.327 Angle : 0.679 9.715 10101 Z= 0.370 Chirality : 0.043 0.219 1139 Planarity : 0.006 0.079 1278 Dihedral : 14.746 176.032 2824 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.37 (0.28), residues: 899 helix: 0.15 (0.24), residues: 441 sheet: 1.23 (0.61), residues: 73 loop : 0.40 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1119 HIS 0.006 0.001 HIS A 461 PHE 0.016 0.002 PHE A 316 TYR 0.015 0.001 TYR A 269 ARG 0.003 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.26259 ( 372) hydrogen bonds : angle 8.10041 ( 1119) metal coordination : bond 0.00514 ( 2) SS BOND : bond 0.00160 ( 3) SS BOND : angle 1.53923 ( 6) covalent geometry : bond 0.00671 ( 7453) covalent geometry : angle 0.67809 (10095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.6323 (mm-30) cc_final: 0.5905 (mt-10) REVERT: A 281 TYR cc_start: 0.8113 (m-10) cc_final: 0.7865 (m-10) REVERT: A 296 MET cc_start: 0.7792 (ttt) cc_final: 0.7290 (ttm) REVERT: A 374 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7577 (mmmt) REVERT: A 432 ASP cc_start: 0.7535 (m-30) cc_final: 0.7311 (m-30) REVERT: A 1015 THR cc_start: 0.7057 (m) cc_final: 0.6737 (m) REVERT: A 1140 HIS cc_start: 0.7853 (t-170) cc_final: 0.7634 (t-170) REVERT: A 1187 LEU cc_start: 0.8247 (mm) cc_final: 0.7885 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1778 time to fit residues: 38.6638 Evaluate side-chains 131 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.0020 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 340 GLN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.207400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167803 restraints weight = 9220.294| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.77 r_work: 0.3579 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7458 Z= 0.180 Angle : 0.616 8.774 10101 Z= 0.329 Chirality : 0.043 0.160 1139 Planarity : 0.005 0.077 1278 Dihedral : 13.073 169.901 1081 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.76 % Allowed : 6.94 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 899 helix: 0.76 (0.23), residues: 469 sheet: 1.05 (0.65), residues: 73 loop : 0.23 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1119 HIS 0.007 0.002 HIS A1266 PHE 0.019 0.002 PHE A1253 TYR 0.012 0.001 TYR A1125 ARG 0.005 0.000 ARG A1097 Details of bonding type rmsd hydrogen bonds : bond 0.06184 ( 372) hydrogen bonds : angle 5.20187 ( 1119) metal coordination : bond 0.00646 ( 2) SS BOND : bond 0.00326 ( 3) SS BOND : angle 1.57044 ( 6) covalent geometry : bond 0.00412 ( 7453) covalent geometry : angle 0.61533 (10095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.774 Fit side-chains REVERT: A 167 TRP cc_start: 0.7559 (t-100) cc_final: 0.6596 (t-100) REVERT: A 221 GLU cc_start: 0.6470 (mm-30) cc_final: 0.5895 (mt-10) REVERT: A 296 MET cc_start: 0.7790 (ttt) cc_final: 0.7283 (ttm) REVERT: A 432 ASP cc_start: 0.7915 (m-30) cc_final: 0.7653 (m-30) REVERT: A 1167 PHE cc_start: 0.8066 (m-10) cc_final: 0.7813 (m-10) REVERT: A 1187 LEU cc_start: 0.8110 (mm) cc_final: 0.7897 (mt) REVERT: A 1247 TYR cc_start: 0.7618 (t80) cc_final: 0.7196 (t80) REVERT: A 1300 TYR cc_start: 0.7737 (m-10) cc_final: 0.7306 (m-80) outliers start: 6 outliers final: 4 residues processed: 151 average time/residue: 0.1749 time to fit residues: 37.4781 Evaluate side-chains 139 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain F residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.204208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164871 restraints weight = 9319.752| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.70 r_work: 0.3507 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7458 Z= 0.213 Angle : 0.619 9.191 10101 Z= 0.327 Chirality : 0.044 0.165 1139 Planarity : 0.005 0.066 1278 Dihedral : 12.896 168.952 1081 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.14 % Allowed : 9.21 % Favored : 88.65 % 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: 0.63 (0.27), residues: 899 helix: 0.79 (0.23), residues: 469 sheet: 0.86 (0.65), residues: 73 loop : -0.01 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1119 HIS 0.007 0.002 HIS A1266 PHE 0.016 0.002 PHE A1080 TYR 0.019 0.002 TYR A1273 ARG 0.002 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 372) hydrogen bonds : angle 4.86700 ( 1119) metal coordination : bond 0.00830 ( 2) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.22002 ( 6) covalent geometry : bond 0.00506 ( 7453) covalent geometry : angle 0.61839 (10095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.737 Fit side-chains REVERT: A 221 GLU cc_start: 0.6304 (mm-30) cc_final: 0.5540 (mt-10) REVERT: A 241 ASP cc_start: 0.8099 (t0) cc_final: 0.7821 (t70) REVERT: A 296 MET cc_start: 0.7611 (ttt) cc_final: 0.7184 (ttm) REVERT: A 436 ARG cc_start: 0.7162 (ptt180) cc_final: 0.6649 (ptt180) REVERT: A 1061 LYS cc_start: 0.7570 (mttt) cc_final: 0.6890 (mmtt) REVERT: A 1084 MET cc_start: 0.8984 (mpp) cc_final: 0.8732 (mpp) REVERT: A 1167 PHE cc_start: 0.8024 (m-10) cc_final: 0.7739 (m-10) REVERT: A 1247 TYR cc_start: 0.7531 (t80) cc_final: 0.7121 (t80) REVERT: A 1255 GLN cc_start: 0.8149 (mt0) cc_final: 0.7765 (mp10) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 0.1613 time to fit residues: 34.1458 Evaluate side-chains 148 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.206901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.167746 restraints weight = 9336.455| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.72 r_work: 0.3547 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7458 Z= 0.126 Angle : 0.542 9.295 10101 Z= 0.282 Chirality : 0.041 0.160 1139 Planarity : 0.005 0.079 1278 Dihedral : 12.636 167.379 1081 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.39 % Allowed : 10.72 % Favored : 87.89 % 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: 1.00 (0.28), residues: 899 helix: 1.19 (0.23), residues: 470 sheet: 0.80 (0.63), residues: 73 loop : 0.07 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1337 HIS 0.007 0.001 HIS A 487 PHE 0.014 0.002 PHE A 316 TYR 0.025 0.001 TYR A1273 ARG 0.001 0.000 ARG A1040 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 372) hydrogen bonds : angle 4.50564 ( 1119) metal coordination : bond 0.00467 ( 2) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.80491 ( 6) covalent geometry : bond 0.00285 ( 7453) covalent geometry : angle 0.54138 (10095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.699 Fit side-chains REVERT: A 167 TRP cc_start: 0.7509 (t-100) cc_final: 0.6575 (t-100) REVERT: A 221 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5593 (mt-10) REVERT: A 230 VAL cc_start: 0.7990 (t) cc_final: 0.7774 (m) REVERT: A 241 ASP cc_start: 0.8071 (t0) cc_final: 0.7799 (t70) REVERT: A 296 MET cc_start: 0.7628 (ttt) cc_final: 0.7324 (ttm) REVERT: A 1015 THR cc_start: 0.6357 (OUTLIER) cc_final: 0.6093 (p) REVERT: A 1061 LYS cc_start: 0.7682 (mttt) cc_final: 0.7006 (mmtt) REVERT: A 1084 MET cc_start: 0.8909 (mpp) cc_final: 0.8539 (mpp) REVERT: A 1255 GLN cc_start: 0.8264 (mt0) cc_final: 0.7844 (mp10) outliers start: 11 outliers final: 8 residues processed: 148 average time/residue: 0.1583 time to fit residues: 33.3488 Evaluate side-chains 138 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.205927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165993 restraints weight = 9245.806| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.64 r_work: 0.3629 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7458 Z= 0.128 Angle : 0.531 9.219 10101 Z= 0.278 Chirality : 0.041 0.152 1139 Planarity : 0.005 0.080 1278 Dihedral : 12.480 167.158 1081 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.89 % Allowed : 11.60 % Favored : 86.51 % 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: 1.11 (0.28), residues: 899 helix: 1.31 (0.24), residues: 477 sheet: 0.72 (0.62), residues: 73 loop : 0.08 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1217 HIS 0.006 0.001 HIS A1266 PHE 0.014 0.002 PHE A 316 TYR 0.021 0.001 TYR A1273 ARG 0.001 0.000 ARG A1040 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 372) hydrogen bonds : angle 4.40026 ( 1119) metal coordination : bond 0.00542 ( 2) SS BOND : bond 0.00136 ( 3) SS BOND : angle 0.64322 ( 6) covalent geometry : bond 0.00296 ( 7453) covalent geometry : angle 0.53090 (10095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.762 Fit side-chains REVERT: A 167 TRP cc_start: 0.7482 (t-100) cc_final: 0.6527 (t-100) REVERT: A 221 GLU cc_start: 0.6271 (mm-30) cc_final: 0.5456 (mt-10) REVERT: A 230 VAL cc_start: 0.7995 (t) cc_final: 0.7780 (m) REVERT: A 296 MET cc_start: 0.7673 (ttt) cc_final: 0.7124 (ttm) REVERT: A 1015 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.6172 (p) REVERT: A 1061 LYS cc_start: 0.7651 (mttt) cc_final: 0.6921 (mmtt) REVERT: A 1152 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8308 (tttp) REVERT: A 1179 GLN cc_start: 0.7865 (mp-120) cc_final: 0.7387 (mp10) REVERT: A 1247 TYR cc_start: 0.7429 (t80) cc_final: 0.7112 (t80) REVERT: A 1255 GLN cc_start: 0.8376 (mt0) cc_final: 0.7894 (mp10) REVERT: A 1326 TYR cc_start: 0.9006 (t80) cc_final: 0.8650 (t80) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 0.1613 time to fit residues: 33.3130 Evaluate side-chains 143 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.209446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169645 restraints weight = 9387.383| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.77 r_work: 0.3570 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7458 Z= 0.139 Angle : 0.545 9.331 10101 Z= 0.282 Chirality : 0.041 0.152 1139 Planarity : 0.005 0.082 1278 Dihedral : 12.431 166.712 1081 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.64 % Allowed : 11.98 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.28), residues: 899 helix: 1.35 (0.24), residues: 477 sheet: 0.70 (0.62), residues: 73 loop : 0.00 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1217 HIS 0.006 0.001 HIS A 487 PHE 0.015 0.002 PHE A 442 TYR 0.019 0.001 TYR A1273 ARG 0.001 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 372) hydrogen bonds : angle 4.34017 ( 1119) metal coordination : bond 0.00667 ( 2) SS BOND : bond 0.00463 ( 3) SS BOND : angle 1.24709 ( 6) covalent geometry : bond 0.00327 ( 7453) covalent geometry : angle 0.54425 (10095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.295 Fit side-chains REVERT: A 221 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5712 (tt0) REVERT: A 230 VAL cc_start: 0.7999 (t) cc_final: 0.7781 (m) REVERT: A 296 MET cc_start: 0.7461 (ttt) cc_final: 0.7055 (ttm) REVERT: A 521 MET cc_start: 0.8484 (mtm) cc_final: 0.8116 (ttp) REVERT: A 1015 THR cc_start: 0.6476 (OUTLIER) cc_final: 0.6194 (p) REVERT: A 1061 LYS cc_start: 0.7608 (mttt) cc_final: 0.6845 (mmtt) REVERT: A 1088 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 1152 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8347 (tttp) REVERT: A 1247 TYR cc_start: 0.7475 (t80) cc_final: 0.7166 (t80) REVERT: A 1255 GLN cc_start: 0.8422 (mt0) cc_final: 0.8010 (mp10) REVERT: A 1326 TYR cc_start: 0.9006 (t80) cc_final: 0.8675 (t80) outliers start: 13 outliers final: 11 residues processed: 143 average time/residue: 0.1610 time to fit residues: 33.5904 Evaluate side-chains 140 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.0050 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.208456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169479 restraints weight = 9266.671| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.75 r_work: 0.3508 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7458 Z= 0.119 Angle : 0.527 9.089 10101 Z= 0.273 Chirality : 0.040 0.146 1139 Planarity : 0.005 0.081 1278 Dihedral : 12.399 167.194 1081 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.89 % Allowed : 12.74 % Favored : 85.37 % 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: 1.26 (0.28), residues: 899 helix: 1.50 (0.24), residues: 477 sheet: 0.80 (0.62), residues: 73 loop : 0.02 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1337 HIS 0.006 0.001 HIS A1266 PHE 0.014 0.001 PHE A1331 TYR 0.028 0.001 TYR A1273 ARG 0.001 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 372) hydrogen bonds : angle 4.24843 ( 1119) metal coordination : bond 0.00495 ( 2) SS BOND : bond 0.00075 ( 3) SS BOND : angle 0.90093 ( 6) covalent geometry : bond 0.00274 ( 7453) covalent geometry : angle 0.52716 (10095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.970 Fit side-chains REVERT: A 167 TRP cc_start: 0.7528 (t-100) cc_final: 0.6583 (t-100) REVERT: A 221 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5632 (mt-10) REVERT: A 230 VAL cc_start: 0.7964 (t) cc_final: 0.7735 (m) REVERT: A 296 MET cc_start: 0.7514 (ttt) cc_final: 0.7200 (ttm) REVERT: A 521 MET cc_start: 0.8417 (mtm) cc_final: 0.8041 (ttp) REVERT: A 1015 THR cc_start: 0.6420 (OUTLIER) cc_final: 0.6152 (p) REVERT: A 1020 PHE cc_start: 0.5744 (m-80) cc_final: 0.5339 (m-80) REVERT: A 1061 LYS cc_start: 0.7453 (mttt) cc_final: 0.6747 (mmtt) REVERT: A 1088 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 1152 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8333 (tttp) REVERT: A 1255 GLN cc_start: 0.8459 (mt0) cc_final: 0.8055 (mp10) REVERT: A 1326 TYR cc_start: 0.9038 (t80) cc_final: 0.8702 (t80) outliers start: 15 outliers final: 10 residues processed: 149 average time/residue: 0.2049 time to fit residues: 43.7729 Evaluate side-chains 142 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.208625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.169861 restraints weight = 9322.049| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.78 r_work: 0.3483 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7458 Z= 0.119 Angle : 0.547 10.127 10101 Z= 0.281 Chirality : 0.040 0.148 1139 Planarity : 0.005 0.082 1278 Dihedral : 12.360 167.221 1081 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.02 % Allowed : 13.37 % Favored : 84.62 % 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: 1.32 (0.29), residues: 899 helix: 1.59 (0.24), residues: 474 sheet: 0.82 (0.63), residues: 73 loop : -0.01 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1337 HIS 0.005 0.001 HIS A1266 PHE 0.013 0.001 PHE A1331 TYR 0.027 0.001 TYR A1273 ARG 0.001 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 372) hydrogen bonds : angle 4.22230 ( 1119) metal coordination : bond 0.00482 ( 2) SS BOND : bond 0.00220 ( 3) SS BOND : angle 1.14408 ( 6) covalent geometry : bond 0.00276 ( 7453) covalent geometry : angle 0.54629 (10095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.158 Fit side-chains REVERT: A 167 TRP cc_start: 0.7540 (t-100) cc_final: 0.6584 (t-100) REVERT: A 230 VAL cc_start: 0.7919 (t) cc_final: 0.7694 (m) REVERT: A 296 MET cc_start: 0.7478 (ttt) cc_final: 0.7044 (ttm) REVERT: A 521 MET cc_start: 0.8379 (mtm) cc_final: 0.7983 (ttp) REVERT: A 1061 LYS cc_start: 0.7417 (mttt) cc_final: 0.6668 (mmtt) REVERT: A 1088 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 1152 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8351 (tttp) outliers start: 16 outliers final: 14 residues processed: 143 average time/residue: 0.1967 time to fit residues: 41.6743 Evaluate side-chains 145 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.206718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167270 restraints weight = 9310.273| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.81 r_work: 0.3447 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7458 Z= 0.151 Angle : 0.567 9.101 10101 Z= 0.294 Chirality : 0.042 0.156 1139 Planarity : 0.005 0.085 1278 Dihedral : 12.375 166.574 1081 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.02 % Allowed : 13.62 % Favored : 84.36 % 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 (0.29), residues: 899 helix: 1.50 (0.24), residues: 474 sheet: 0.73 (0.62), residues: 73 loop : -0.04 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1217 HIS 0.005 0.002 HIS A 461 PHE 0.013 0.002 PHE A 442 TYR 0.026 0.001 TYR A1273 ARG 0.002 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 372) hydrogen bonds : angle 4.28354 ( 1119) metal coordination : bond 0.00944 ( 2) SS BOND : bond 0.00224 ( 3) SS BOND : angle 1.53585 ( 6) covalent geometry : bond 0.00360 ( 7453) covalent geometry : angle 0.56622 (10095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.830 Fit side-chains REVERT: A 109 CYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7787 (p) REVERT: A 167 TRP cc_start: 0.7549 (t-100) cc_final: 0.6643 (t-100) REVERT: A 230 VAL cc_start: 0.7911 (t) cc_final: 0.7669 (m) REVERT: A 275 TRP cc_start: 0.7655 (m100) cc_final: 0.6646 (m100) REVERT: A 296 MET cc_start: 0.7240 (ttt) cc_final: 0.6990 (ttm) REVERT: A 1061 LYS cc_start: 0.7382 (mttt) cc_final: 0.6676 (mmtt) REVERT: A 1088 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: A 1152 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8352 (tttp) outliers start: 16 outliers final: 13 residues processed: 142 average time/residue: 0.1606 time to fit residues: 32.5901 Evaluate side-chains 146 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.211718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.171881 restraints weight = 9436.159| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.80 r_work: 0.3520 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7458 Z= 0.114 Angle : 0.552 10.708 10101 Z= 0.282 Chirality : 0.040 0.142 1139 Planarity : 0.005 0.083 1278 Dihedral : 12.335 166.875 1081 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.77 % Allowed : 14.00 % Favored : 84.24 % 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: 1.36 (0.29), residues: 899 helix: 1.63 (0.24), residues: 477 sheet: 0.85 (0.63), residues: 73 loop : -0.02 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1337 HIS 0.005 0.001 HIS A1140 PHE 0.013 0.001 PHE A1331 TYR 0.025 0.001 TYR A1273 ARG 0.001 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 372) hydrogen bonds : angle 4.16685 ( 1119) metal coordination : bond 0.00570 ( 2) SS BOND : bond 0.00193 ( 3) SS BOND : angle 1.05258 ( 6) covalent geometry : bond 0.00260 ( 7453) covalent geometry : angle 0.55167 (10095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7774 (p) REVERT: A 127 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5779 (p90) REVERT: A 167 TRP cc_start: 0.7517 (t-100) cc_final: 0.6482 (t-100) REVERT: A 230 VAL cc_start: 0.7911 (t) cc_final: 0.7694 (m) REVERT: A 275 TRP cc_start: 0.7637 (m100) cc_final: 0.6631 (m100) REVERT: A 296 MET cc_start: 0.7519 (ttt) cc_final: 0.7178 (ttm) REVERT: A 1015 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.6145 (p) REVERT: A 1061 LYS cc_start: 0.7403 (mttt) cc_final: 0.6675 (mmtt) REVERT: A 1152 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8376 (tttp) outliers start: 14 outliers final: 9 residues processed: 147 average time/residue: 0.1581 time to fit residues: 33.0544 Evaluate side-chains 147 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain F residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 HIS F 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.209870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.170077 restraints weight = 9290.400| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.78 r_work: 0.3467 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7458 Z= 0.140 Angle : 0.562 8.990 10101 Z= 0.290 Chirality : 0.041 0.141 1139 Planarity : 0.005 0.084 1278 Dihedral : 12.324 166.644 1081 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.39 % Allowed : 14.25 % Favored : 84.36 % 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: 1.28 (0.29), residues: 899 helix: 1.57 (0.24), residues: 477 sheet: 0.76 (0.62), residues: 73 loop : -0.04 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1217 HIS 0.005 0.001 HIS A1266 PHE 0.013 0.002 PHE A 442 TYR 0.025 0.001 TYR A1273 ARG 0.002 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 372) hydrogen bonds : angle 4.20427 ( 1119) metal coordination : bond 0.00726 ( 2) SS BOND : bond 0.00229 ( 3) SS BOND : angle 1.27851 ( 6) covalent geometry : bond 0.00333 ( 7453) covalent geometry : angle 0.56140 (10095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.77 seconds wall clock time: 65 minutes 55.37 seconds (3955.37 seconds total)