Starting phenix.real_space_refine on Mon Jul 28 14:42:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kar_22781/07_2025/7kar_22781.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kar_22781/07_2025/7kar_22781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kar_22781/07_2025/7kar_22781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kar_22781/07_2025/7kar_22781.map" model { file = "/net/cci-nas-00/data/ceres_data/7kar_22781/07_2025/7kar_22781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kar_22781/07_2025/7kar_22781.cif" } resolution = 4.0 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= 0.003 sd= 0.051 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 42 5.16 5 C 6811 2.51 5 N 1755 2.21 5 O 1827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10435 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3362 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.81, per 1000 atoms: 0.56 Number of scatterers: 10435 At special positions: 0 Unit cell: (110.67, 127.33, 138.04, 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 42 16.00 O 1827 8.00 N 1755 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 66.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.807A pdb=" N TRP A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 107 through 137 removed outlier: 4.072A pdb=" N ARG A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.803A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.424A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.740A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.214A pdb=" N ILE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.581A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.732A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.845A pdb=" N GLY B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.985A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.016A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.752A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.754A pdb=" N SER D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.659A pdb=" N ALA D 259 " --> pdb=" O HIS D 255 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.730A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.785A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.873A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 4.039A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.120A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.638A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.210A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.401A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.780A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 123 removed outlier: 3.741A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.773A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 3.919A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.402A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.607A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.508A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.994A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 4.057A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.768A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 3.991A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434 removed outlier: 7.014A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 571 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 6 647 hydrogen bonds defined for protein. 1908 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: 3.31 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3280 1.34 - 1.46: 1859 1.46 - 1.57: 5437 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 10643 Sorted by residual: bond pdb=" C ILE D 531 " pdb=" N ILE D 532 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.52e-02 4.33e+03 1.54e+00 bond pdb=" CG1 ILE D 280 " pdb=" CD1 ILE D 280 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.42e+00 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.14e+00 bond pdb=" C VAL D 215 " pdb=" O VAL D 215 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 6.00e-01 ... (remaining 10638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 14104 1.58 - 3.16: 268 3.16 - 4.75: 34 4.75 - 6.33: 16 6.33 - 7.91: 4 Bond angle restraints: 14426 Sorted by residual: angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 113.42 109.59 3.83 1.17e+00 7.31e-01 1.07e+01 angle pdb=" C HIS D 424 " pdb=" N ILE D 425 " pdb=" CA ILE D 425 " ideal model delta sigma weight residual 122.59 120.24 2.35 7.20e-01 1.93e+00 1.06e+01 angle pdb=" N ILE E 126 " pdb=" CA ILE E 126 " pdb=" C ILE E 126 " ideal model delta sigma weight residual 113.71 110.65 3.06 9.50e-01 1.11e+00 1.04e+01 angle pdb=" C THR D 595 " pdb=" N ASP D 596 " pdb=" CA ASP D 596 " ideal model delta sigma weight residual 122.08 118.00 4.08 1.53e+00 4.27e-01 7.11e+00 angle pdb=" N ASN A 290 " pdb=" CA ASN A 290 " pdb=" C ASN A 290 " ideal model delta sigma weight residual 111.14 113.99 -2.85 1.08e+00 8.57e-01 6.95e+00 ... (remaining 14421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 5845 17.03 - 34.07: 471 34.07 - 51.10: 77 51.10 - 68.13: 10 68.13 - 85.17: 8 Dihedral angle restraints: 6411 sinusoidal: 2516 harmonic: 3895 Sorted by residual: dihedral pdb=" CA LEU F 153 " pdb=" C LEU F 153 " pdb=" N ARG F 154 " pdb=" CA ARG F 154 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ILE D 425 " pdb=" C ILE D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual -180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA VAL D 437 " pdb=" C VAL D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta harmonic sigma weight residual 180.00 163.84 16.16 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 952 0.027 - 0.054: 501 0.054 - 0.080: 150 0.080 - 0.107: 83 0.107 - 0.134: 24 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CA THR A 291 " pdb=" N THR A 291 " pdb=" C THR A 291 " pdb=" CB THR A 291 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE D 573 " pdb=" N ILE D 573 " pdb=" C ILE D 573 " pdb=" CB ILE D 573 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1707 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO F 48 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 291 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 292 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO F 94 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.018 5.00e-02 4.00e+02 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1789 2.76 - 3.29: 10529 3.29 - 3.83: 16505 3.83 - 4.36: 17746 4.36 - 4.90: 31019 Nonbonded interactions: 77588 Sorted by model distance: nonbonded pdb=" OH TYR E 121 " pdb=" OE1 GLU E 128 " model vdw 2.224 3.040 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.234 3.120 nonbonded pdb=" O SER A 444 " pdb=" OG SER A 447 " model vdw 2.264 3.040 nonbonded pdb=" NZ LYS A 273 " pdb=" O GLN A 398 " model vdw 2.281 3.120 nonbonded pdb=" ND2 ASN D 55 " pdb=" O LEU D 496 " model vdw 2.281 3.120 ... (remaining 77583 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 group one per residue 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 25.600 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10643 Z= 0.158 Angle : 0.591 7.909 14426 Z= 0.334 Chirality : 0.039 0.134 1710 Planarity : 0.003 0.039 1793 Dihedral : 12.735 85.166 3883 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.22), residues: 1317 helix: 0.12 (0.17), residues: 795 sheet: -2.85 (0.42), residues: 106 loop : -2.37 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 513 HIS 0.005 0.001 HIS B 72 PHE 0.016 0.001 PHE D 343 TYR 0.018 0.001 TYR F 190 ARG 0.002 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.13434 ( 637) hydrogen bonds : angle 5.01655 ( 1908) covalent geometry : bond 0.00342 (10643) covalent geometry : angle 0.59116 (14426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7016 (m-90) cc_final: 0.6679 (m-10) REVERT: C 45 LYS cc_start: 0.8722 (mttm) cc_final: 0.8405 (mttp) REVERT: D 22 LEU cc_start: 0.9296 (mt) cc_final: 0.9002 (pp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2319 time to fit residues: 36.3468 Evaluate side-chains 63 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN D 424 HIS D 427 ASN D 494 GLN E 88 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.065144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047995 restraints weight = 55730.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047968 restraints weight = 32761.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048111 restraints weight = 24511.407| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10643 Z= 0.265 Angle : 0.692 11.633 14426 Z= 0.348 Chirality : 0.042 0.163 1710 Planarity : 0.004 0.045 1793 Dihedral : 3.995 22.981 1422 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.80 % Allowed : 12.13 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.23), residues: 1317 helix: 1.15 (0.18), residues: 814 sheet: -2.54 (0.43), residues: 106 loop : -1.80 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 513 HIS 0.006 0.001 HIS C 72 PHE 0.018 0.002 PHE D 356 TYR 0.020 0.002 TYR F 190 ARG 0.006 0.001 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 637) hydrogen bonds : angle 4.34558 ( 1908) covalent geometry : bond 0.00600 (10643) covalent geometry : angle 0.69182 (14426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7844 (m-90) cc_final: 0.7213 (m-10) REVERT: A 249 MET cc_start: 0.9153 (mtm) cc_final: 0.8752 (ttp) REVERT: C 45 LYS cc_start: 0.8921 (mttm) cc_final: 0.8663 (mttp) outliers start: 20 outliers final: 10 residues processed: 88 average time/residue: 0.1697 time to fit residues: 23.8022 Evaluate side-chains 70 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN D 494 GLN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.067464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050591 restraints weight = 59963.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051287 restraints weight = 34288.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051257 restraints weight = 24758.715| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10643 Z= 0.129 Angle : 0.562 9.382 14426 Z= 0.278 Chirality : 0.039 0.147 1710 Planarity : 0.004 0.046 1793 Dihedral : 3.734 21.222 1422 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.17 % Allowed : 14.73 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1317 helix: 1.75 (0.18), residues: 819 sheet: -2.16 (0.49), residues: 94 loop : -1.29 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 PHE 0.010 0.001 PHE D 356 TYR 0.021 0.001 TYR C 47 ARG 0.002 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 637) hydrogen bonds : angle 3.78888 ( 1908) covalent geometry : bond 0.00291 (10643) covalent geometry : angle 0.56188 (14426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9203 (mmp) cc_final: 0.8706 (mmt) REVERT: A 249 MET cc_start: 0.9060 (mtm) cc_final: 0.8669 (ttp) REVERT: C 45 LYS cc_start: 0.8942 (mttm) cc_final: 0.8735 (mttp) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.1845 time to fit residues: 24.1217 Evaluate side-chains 71 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.0070 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.068757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051761 restraints weight = 58755.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052914 restraints weight = 33926.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.053834 restraints weight = 21528.651| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10643 Z= 0.101 Angle : 0.544 11.077 14426 Z= 0.264 Chirality : 0.038 0.141 1710 Planarity : 0.003 0.050 1793 Dihedral : 3.487 17.895 1422 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.08 % Allowed : 14.82 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.24), residues: 1317 helix: 1.99 (0.19), residues: 822 sheet: -1.50 (0.53), residues: 92 loop : -0.91 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.007 0.001 HIS D 309 PHE 0.007 0.001 PHE A 92 TYR 0.010 0.001 TYR F 190 ARG 0.002 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 637) hydrogen bonds : angle 3.48112 ( 1908) covalent geometry : bond 0.00212 (10643) covalent geometry : angle 0.54433 (14426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9305 (tpt) cc_final: 0.9079 (mmm) REVERT: A 158 MET cc_start: 0.9152 (mmp) cc_final: 0.8593 (mmt) REVERT: A 249 MET cc_start: 0.8998 (mtm) cc_final: 0.8596 (ttp) outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 0.1784 time to fit residues: 25.6718 Evaluate side-chains 70 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.068044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051370 restraints weight = 59350.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052098 restraints weight = 33565.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.052026 restraints weight = 24992.004| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10643 Z= 0.115 Angle : 0.554 11.002 14426 Z= 0.270 Chirality : 0.038 0.142 1710 Planarity : 0.003 0.053 1793 Dihedral : 3.462 17.854 1422 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 15.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.24), residues: 1317 helix: 2.08 (0.19), residues: 820 sheet: -1.20 (0.59), residues: 86 loop : -0.76 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 PHE 0.019 0.001 PHE A 159 TYR 0.020 0.001 TYR C 47 ARG 0.002 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 637) hydrogen bonds : angle 3.52443 ( 1908) covalent geometry : bond 0.00260 (10643) covalent geometry : angle 0.55378 (14426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9343 (tpt) cc_final: 0.9128 (mmm) REVERT: A 158 MET cc_start: 0.9206 (mmp) cc_final: 0.8555 (mmt) REVERT: A 249 MET cc_start: 0.8991 (mtm) cc_final: 0.8592 (ttp) REVERT: F 87 MET cc_start: 0.8692 (ttt) cc_final: 0.8480 (tmm) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 0.1806 time to fit residues: 23.5180 Evaluate side-chains 73 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.067299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050471 restraints weight = 55831.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.050898 restraints weight = 28647.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051066 restraints weight = 21986.782| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10643 Z= 0.114 Angle : 0.571 12.156 14426 Z= 0.273 Chirality : 0.039 0.167 1710 Planarity : 0.003 0.053 1793 Dihedral : 3.471 18.096 1422 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.26 % Allowed : 16.98 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.24), residues: 1317 helix: 2.11 (0.19), residues: 821 sheet: -1.07 (0.60), residues: 86 loop : -0.58 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 PHE 0.017 0.001 PHE B 64 TYR 0.014 0.001 TYR C 47 ARG 0.001 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 637) hydrogen bonds : angle 3.49373 ( 1908) covalent geometry : bond 0.00257 (10643) covalent geometry : angle 0.57097 (14426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9337 (tpt) cc_final: 0.9108 (mmm) REVERT: A 158 MET cc_start: 0.9177 (mmp) cc_final: 0.8556 (mmt) REVERT: A 249 MET cc_start: 0.8993 (mtm) cc_final: 0.8596 (ttp) REVERT: A 281 TYR cc_start: 0.9385 (t80) cc_final: 0.9102 (t80) outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 0.1687 time to fit residues: 22.5872 Evaluate side-chains 73 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.065489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048231 restraints weight = 57281.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048550 restraints weight = 31470.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048707 restraints weight = 23564.623| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10643 Z= 0.197 Angle : 0.634 11.821 14426 Z= 0.310 Chirality : 0.040 0.140 1710 Planarity : 0.004 0.056 1793 Dihedral : 3.699 18.878 1422 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.16 % Allowed : 17.43 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.24), residues: 1317 helix: 2.05 (0.19), residues: 817 sheet: -1.32 (0.55), residues: 98 loop : -0.53 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 513 HIS 0.005 0.001 HIS C 72 PHE 0.015 0.001 PHE D 356 TYR 0.016 0.001 TYR F 190 ARG 0.003 0.000 ARG D 510 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 637) hydrogen bonds : angle 3.77760 ( 1908) covalent geometry : bond 0.00447 (10643) covalent geometry : angle 0.63438 (14426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.7655 (m-90) REVERT: A 158 MET cc_start: 0.9193 (mmp) cc_final: 0.8530 (mmt) REVERT: A 249 MET cc_start: 0.9024 (mtm) cc_final: 0.8616 (ttp) REVERT: D 343 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8541 (t80) outliers start: 24 outliers final: 15 residues processed: 88 average time/residue: 0.1838 time to fit residues: 26.0646 Evaluate side-chains 80 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.066823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049916 restraints weight = 54948.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050381 restraints weight = 28707.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050497 restraints weight = 21786.452| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10643 Z= 0.127 Angle : 0.589 12.941 14426 Z= 0.283 Chirality : 0.039 0.144 1710 Planarity : 0.003 0.055 1793 Dihedral : 3.572 18.241 1422 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.71 % Allowed : 18.24 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.24), residues: 1317 helix: 2.12 (0.19), residues: 823 sheet: -1.25 (0.55), residues: 98 loop : -0.46 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.004 0.001 HIS D 309 PHE 0.021 0.001 PHE A 92 TYR 0.012 0.001 TYR F 190 ARG 0.001 0.000 ARG D 510 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 637) hydrogen bonds : angle 3.58365 ( 1908) covalent geometry : bond 0.00289 (10643) covalent geometry : angle 0.58948 (14426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.7703 (m-90) REVERT: A 158 MET cc_start: 0.9180 (mmp) cc_final: 0.8516 (mmt) REVERT: A 236 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 249 MET cc_start: 0.8998 (mtm) cc_final: 0.8589 (ttp) REVERT: D 343 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8529 (t80) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.1648 time to fit residues: 21.8185 Evaluate side-chains 79 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 188 ASN D 520 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.067330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050535 restraints weight = 55833.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051071 restraints weight = 28735.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051199 restraints weight = 21448.486| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10643 Z= 0.108 Angle : 0.588 12.623 14426 Z= 0.279 Chirality : 0.039 0.139 1710 Planarity : 0.003 0.051 1793 Dihedral : 3.457 18.434 1422 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.44 % Allowed : 18.42 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.25), residues: 1317 helix: 2.19 (0.19), residues: 826 sheet: -0.91 (0.61), residues: 86 loop : -0.37 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 PHE 0.020 0.001 PHE A 92 TYR 0.012 0.001 TYR F 190 ARG 0.001 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 637) hydrogen bonds : angle 3.49738 ( 1908) covalent geometry : bond 0.00243 (10643) covalent geometry : angle 0.58782 (14426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7985 (OUTLIER) cc_final: 0.7745 (m-90) REVERT: A 158 MET cc_start: 0.9193 (mmp) cc_final: 0.8570 (mmt) REVERT: A 236 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8099 (t80) REVERT: A 249 MET cc_start: 0.8965 (mtm) cc_final: 0.8552 (ttp) REVERT: D 343 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8519 (t80) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.2456 time to fit residues: 33.3662 Evaluate side-chains 77 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.067322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050524 restraints weight = 55643.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051028 restraints weight = 29011.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051154 restraints weight = 21546.322| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 10643 Z= 0.167 Angle : 0.954 59.194 14426 Z= 0.527 Chirality : 0.040 0.345 1710 Planarity : 0.005 0.135 1793 Dihedral : 3.459 18.429 1422 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.44 % Allowed : 18.51 % Favored : 80.05 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.25), residues: 1317 helix: 2.18 (0.19), residues: 826 sheet: -0.89 (0.61), residues: 86 loop : -0.35 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 PHE 0.015 0.001 PHE A 92 TYR 0.011 0.001 TYR F 190 ARG 0.001 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 637) hydrogen bonds : angle 3.51594 ( 1908) covalent geometry : bond 0.00353 (10643) covalent geometry : angle 0.95389 (14426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.7695 (m-90) REVERT: A 158 MET cc_start: 0.9173 (mmp) cc_final: 0.8546 (mmt) REVERT: A 236 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 249 MET cc_start: 0.8941 (mtm) cc_final: 0.8529 (ttp) REVERT: D 343 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8540 (t80) outliers start: 16 outliers final: 8 residues processed: 83 average time/residue: 0.1681 time to fit residues: 22.6301 Evaluate side-chains 76 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.0040 chunk 102 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.067409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050760 restraints weight = 55361.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051122 restraints weight = 27433.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051487 restraints weight = 20829.644| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 10643 Z= 0.167 Angle : 0.954 59.194 14426 Z= 0.527 Chirality : 0.040 0.345 1710 Planarity : 0.005 0.135 1793 Dihedral : 3.459 18.429 1422 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.08 % Allowed : 18.96 % Favored : 79.96 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.25), residues: 1317 helix: 2.18 (0.19), residues: 826 sheet: -0.89 (0.61), residues: 86 loop : -0.35 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 PHE 0.015 0.001 PHE A 92 TYR 0.011 0.001 TYR F 190 ARG 0.001 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 637) hydrogen bonds : angle 3.51594 ( 1908) covalent geometry : bond 0.00353 (10643) covalent geometry : angle 0.95389 (14426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2933.79 seconds wall clock time: 51 minutes 51.89 seconds (3111.89 seconds total)