Starting phenix.real_space_refine on Wed Mar 4 03:20:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kar_22781/03_2026/7kar_22781.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kar_22781/03_2026/7kar_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_22781/03_2026/7kar_22781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kar_22781/03_2026/7kar_22781.map" model { file = "/net/cci-nas-00/data/ceres_data/7kar_22781/03_2026/7kar_22781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kar_22781/03_2026/7kar_22781.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 1, 'PHE: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: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1} 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: {'GLU:plan': 3, 'GLN:plan1': 1, '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: 2.34, per 1000 atoms: 0.22 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: 0.81 Conformation dependent library (CDL) restraints added in 403.7 milliseconds 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: 0.30 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: 1.47 Time building geometry restraints manager: 1.10 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG E 106 TYR 0.018 0.001 TYR F 190 PHE 0.016 0.001 PHE D 343 TRP 0.013 0.001 TRP D 513 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00342 (10643) covalent geometry : angle 0.59116 (14426) hydrogen bonds : bond 0.13434 ( 637) hydrogen bonds : angle 5.01655 ( 1908) *********************** 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 : 0.443 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: A 65 TRP cc_start: 0.7016 (m-90) cc_final: 0.6676 (m-10) REVERT: A 449 LEU cc_start: 0.9633 (pp) cc_final: 0.9283 (pp) REVERT: C 45 LYS cc_start: 0.8722 (mttm) cc_final: 0.8402 (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: 0.0982 time to fit residues: 15.5271 Evaluate side-chains 62 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 290 ASN D 427 ASN D 494 GLN E 88 HIS E 181 GLN F 68 ASN F 89 GLN F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.067159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049265 restraints weight = 55088.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050517 restraints weight = 32511.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051432 restraints weight = 20863.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051475 restraints weight = 18349.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051417 restraints weight = 16602.841| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10643 Z= 0.134 Angle : 0.583 12.176 14426 Z= 0.288 Chirality : 0.039 0.141 1710 Planarity : 0.004 0.041 1793 Dihedral : 3.659 19.784 1422 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.08 % Allowed : 10.51 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1317 helix: 1.24 (0.18), residues: 818 sheet: -2.45 (0.46), residues: 94 loop : -1.70 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 145 TYR 0.015 0.001 TYR C 47 PHE 0.009 0.001 PHE A 368 TRP 0.007 0.001 TRP F 95 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00302 (10643) covalent geometry : angle 0.58311 (14426) hydrogen bonds : bond 0.03945 ( 637) hydrogen bonds : angle 3.93137 ( 1908) *********************** 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 86 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7410 (m-90) cc_final: 0.6858 (m-10) REVERT: A 249 MET cc_start: 0.9093 (mtm) cc_final: 0.8685 (ttp) REVERT: A 294 MET cc_start: 0.8783 (ptm) cc_final: 0.8547 (ppp) REVERT: C 45 LYS cc_start: 0.8813 (mttm) cc_final: 0.8527 (mttp) REVERT: B 59 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: D 22 LEU cc_start: 0.9347 (mt) cc_final: 0.9054 (pp) REVERT: F 57 MET cc_start: 0.8977 (ttm) cc_final: 0.8714 (tpt) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.0795 time to fit residues: 10.7035 Evaluate side-chains 69 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 117 ILE 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 61 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN D 494 GLN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.066270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049367 restraints weight = 56425.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049131 restraints weight = 33564.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049629 restraints weight = 24386.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049804 restraints weight = 21423.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049877 restraints weight = 19761.865| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10643 Z= 0.160 Angle : 0.580 9.860 14426 Z= 0.287 Chirality : 0.040 0.147 1710 Planarity : 0.004 0.043 1793 Dihedral : 3.715 20.497 1422 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.53 % Allowed : 12.94 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1317 helix: 1.69 (0.18), residues: 817 sheet: -1.99 (0.47), residues: 104 loop : -1.28 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 92 TYR 0.022 0.001 TYR C 47 PHE 0.013 0.001 PHE B 64 TRP 0.009 0.001 TRP D 513 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00362 (10643) covalent geometry : angle 0.57986 (14426) hydrogen bonds : bond 0.03888 ( 637) hydrogen bonds : angle 3.82913 ( 1908) *********************** 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 85 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9222 (mmp) cc_final: 0.8685 (mmt) REVERT: A 249 MET cc_start: 0.9063 (mtm) cc_final: 0.8662 (ttp) REVERT: C 45 LYS cc_start: 0.8934 (mttm) cc_final: 0.8728 (mttp) REVERT: B 59 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: F 57 MET cc_start: 0.9152 (ttm) cc_final: 0.8861 (tpt) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.0690 time to fit residues: 9.3858 Evaluate side-chains 70 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 12 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.067735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051082 restraints weight = 59763.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051594 restraints weight = 35206.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051640 restraints weight = 25085.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.052080 restraints weight = 24163.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052092 restraints weight = 21670.276| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10643 Z= 0.124 Angle : 0.553 8.771 14426 Z= 0.270 Chirality : 0.039 0.147 1710 Planarity : 0.003 0.044 1793 Dihedral : 3.611 20.678 1422 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.62 % Allowed : 13.93 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1317 helix: 1.95 (0.19), residues: 824 sheet: -1.68 (0.53), residues: 94 loop : -0.94 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 92 TYR 0.013 0.001 TYR F 190 PHE 0.009 0.001 PHE D 356 TRP 0.008 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00278 (10643) covalent geometry : angle 0.55285 (14426) hydrogen bonds : bond 0.03532 ( 637) hydrogen bonds : angle 3.61331 ( 1908) *********************** 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 90 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9341 (tpt) cc_final: 0.9093 (mmm) REVERT: A 158 MET cc_start: 0.9206 (mmp) cc_final: 0.8680 (mmt) REVERT: A 249 MET cc_start: 0.9014 (mtm) cc_final: 0.8621 (ttp) REVERT: D 343 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8273 (t80) REVERT: F 57 MET cc_start: 0.9115 (ttm) cc_final: 0.8824 (tpt) outliers start: 18 outliers final: 11 residues processed: 89 average time/residue: 0.0715 time to fit residues: 10.2193 Evaluate side-chains 78 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 516 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 Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN D 311 ASN D 424 HIS ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046969 restraints weight = 57422.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047263 restraints weight = 32716.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047585 restraints weight = 24080.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047746 restraints weight = 22067.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047766 restraints weight = 20236.717| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10643 Z= 0.282 Angle : 0.704 8.567 14426 Z= 0.353 Chirality : 0.042 0.178 1710 Planarity : 0.004 0.053 1793 Dihedral : 4.060 24.099 1422 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 15.45 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1317 helix: 1.73 (0.18), residues: 816 sheet: -1.86 (0.49), residues: 106 loop : -0.89 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 510 TYR 0.024 0.002 TYR C 47 PHE 0.024 0.002 PHE D 356 TRP 0.015 0.002 TRP D 513 HIS 0.007 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00630 (10643) covalent geometry : angle 0.70357 (14426) hydrogen bonds : bond 0.04507 ( 637) hydrogen bonds : angle 4.17045 ( 1908) *********************** 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 90 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9109 (mmp) cc_final: 0.8557 (mmt) REVERT: A 450 MET cc_start: 0.8714 (mmm) cc_final: 0.8450 (tpp) REVERT: D 343 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8476 (t80) REVERT: F 57 MET cc_start: 0.9143 (ttm) cc_final: 0.8850 (tpt) outliers start: 24 outliers final: 19 residues processed: 87 average time/residue: 0.0712 time to fit residues: 10.1932 Evaluate side-chains 79 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 424 PHE 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 355 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 514 CYS 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 117 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.066631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050066 restraints weight = 55538.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049823 restraints weight = 32939.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.050262 restraints weight = 25155.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050418 restraints weight = 22272.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.050499 restraints weight = 19657.907| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10643 Z= 0.133 Angle : 0.584 10.223 14426 Z= 0.285 Chirality : 0.039 0.136 1710 Planarity : 0.004 0.045 1793 Dihedral : 3.765 23.842 1422 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 17.07 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.24), residues: 1317 helix: 2.01 (0.19), residues: 822 sheet: -1.63 (0.50), residues: 104 loop : -0.73 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 186 TYR 0.014 0.001 TYR C 47 PHE 0.021 0.001 PHE B 64 TRP 0.010 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00301 (10643) covalent geometry : angle 0.58407 (14426) hydrogen bonds : bond 0.03666 ( 637) hydrogen bonds : angle 3.70908 ( 1908) *********************** 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 88 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9119 (mmp) cc_final: 0.8539 (mmt) REVERT: A 249 MET cc_start: 0.9062 (mtm) cc_final: 0.8669 (ttp) REVERT: D 343 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8486 (t80) REVERT: F 57 MET cc_start: 0.9165 (ttm) cc_final: 0.8841 (tpt) outliers start: 21 outliers final: 14 residues processed: 87 average time/residue: 0.0696 time to fit residues: 9.8466 Evaluate side-chains 79 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE 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 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 514 CYS 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 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 0.0000 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 overall best weight: 3.9992 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.062776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.045495 restraints weight = 57440.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045388 restraints weight = 35398.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045665 restraints weight = 26900.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.045848 restraints weight = 24321.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045952 restraints weight = 22358.757| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10643 Z= 0.232 Angle : 0.669 10.817 14426 Z= 0.331 Chirality : 0.042 0.204 1710 Planarity : 0.004 0.044 1793 Dihedral : 4.008 28.626 1422 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.25 % Allowed : 17.79 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1317 helix: 1.89 (0.18), residues: 817 sheet: -1.59 (0.53), residues: 98 loop : -0.69 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 510 TYR 0.016 0.001 TYR C 47 PHE 0.019 0.001 PHE D 356 TRP 0.013 0.001 TRP D 513 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00525 (10643) covalent geometry : angle 0.66928 (14426) hydrogen bonds : bond 0.04266 ( 637) hydrogen bonds : angle 4.02992 ( 1908) *********************** 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 91 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9078 (mtm) cc_final: 0.8659 (ttp) REVERT: D 343 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8538 (t80) REVERT: F 57 MET cc_start: 0.9142 (ttm) cc_final: 0.8837 (tpt) outliers start: 25 outliers final: 21 residues processed: 89 average time/residue: 0.0676 time to fit residues: 10.0491 Evaluate side-chains 83 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE 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 C residue 63 ILE 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 355 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 514 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS D 520 GLN D 558 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046895 restraints weight = 55843.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047812 restraints weight = 34210.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.048866 restraints weight = 22576.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048834 restraints weight = 19999.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048834 restraints weight = 17800.393| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10643 Z= 0.109 Angle : 0.600 11.543 14426 Z= 0.285 Chirality : 0.039 0.142 1710 Planarity : 0.004 0.039 1793 Dihedral : 3.705 27.430 1422 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.53 % Allowed : 19.05 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.25), residues: 1317 helix: 2.10 (0.19), residues: 822 sheet: -1.43 (0.54), residues: 98 loop : -0.52 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.012 0.001 TYR C 47 PHE 0.026 0.001 PHE B 64 TRP 0.010 0.001 TRP A 380 HIS 0.007 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00237 (10643) covalent geometry : angle 0.59952 (14426) hydrogen bonds : bond 0.03409 ( 637) hydrogen bonds : angle 3.58277 ( 1908) *********************** 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 93 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8950 (mmt) cc_final: 0.8605 (mmt) REVERT: A 249 MET cc_start: 0.9046 (mtm) cc_final: 0.8657 (ttp) REVERT: D 343 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8531 (t80) REVERT: F 57 MET cc_start: 0.9011 (ttm) cc_final: 0.8808 (tpt) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.0674 time to fit residues: 9.9462 Evaluate side-chains 82 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 103 VAL 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 377 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 86 optimal weight: 0.1980 chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047544 restraints weight = 56950.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048144 restraints weight = 33525.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048352 restraints weight = 23536.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048510 restraints weight = 23072.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048604 restraints weight = 20226.382| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10643 Z= 0.108 Angle : 0.600 11.439 14426 Z= 0.287 Chirality : 0.039 0.169 1710 Planarity : 0.004 0.039 1793 Dihedral : 3.623 27.041 1422 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.08 % Allowed : 19.86 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1317 helix: 2.05 (0.18), residues: 824 sheet: -1.34 (0.55), residues: 99 loop : -0.44 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.012 0.001 TYR C 47 PHE 0.047 0.001 PHE A 159 TRP 0.009 0.001 TRP A 380 HIS 0.011 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00237 (10643) covalent geometry : angle 0.59953 (14426) hydrogen bonds : bond 0.03339 ( 637) hydrogen bonds : angle 3.55934 ( 1908) *********************** 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 82 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9045 (mtm) cc_final: 0.8663 (ttp) REVERT: D 343 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8573 (t80) outliers start: 12 outliers final: 10 residues processed: 81 average time/residue: 0.0594 time to fit residues: 8.0537 Evaluate side-chains 78 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain C residue 44 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 377 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 D residue 555 LEU Chi-restraints excluded: chain E residue 98 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.9990 chunk 87 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 85 optimal weight: 0.0020 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 40.0000 chunk 125 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046772 restraints weight = 59263.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047239 restraints weight = 35771.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047483 restraints weight = 25421.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.047630 restraints weight = 25030.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047723 restraints weight = 21960.634| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10643 Z= 0.112 Angle : 0.598 12.007 14426 Z= 0.286 Chirality : 0.039 0.147 1710 Planarity : 0.004 0.041 1793 Dihedral : 3.593 26.686 1422 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 20.22 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1317 helix: 2.08 (0.18), residues: 826 sheet: -1.22 (0.56), residues: 98 loop : -0.35 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 510 TYR 0.013 0.001 TYR F 190 PHE 0.057 0.001 PHE A 159 TRP 0.009 0.001 TRP A 380 HIS 0.006 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00251 (10643) covalent geometry : angle 0.59840 (14426) hydrogen bonds : bond 0.03338 ( 637) hydrogen bonds : angle 3.57193 ( 1908) ********************** 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 78 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9047 (mtm) cc_final: 0.8667 (ttp) REVERT: D 343 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8592 (t80) REVERT: D 491 MET cc_start: 0.8304 (ttm) cc_final: 0.7474 (tpp) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.0698 time to fit residues: 8.8267 Evaluate side-chains 77 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 377 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046511 restraints weight = 58817.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047041 restraints weight = 35368.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047058 restraints weight = 25465.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047253 restraints weight = 24780.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047343 restraints weight = 23168.934| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10643 Z= 0.118 Angle : 0.605 12.019 14426 Z= 0.289 Chirality : 0.039 0.146 1710 Planarity : 0.004 0.042 1793 Dihedral : 3.571 26.766 1422 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.99 % Allowed : 20.22 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1317 helix: 2.08 (0.18), residues: 826 sheet: -1.22 (0.57), residues: 99 loop : -0.34 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 510 TYR 0.013 0.001 TYR F 190 PHE 0.054 0.001 PHE A 159 TRP 0.009 0.001 TRP A 380 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00267 (10643) covalent geometry : angle 0.60491 (14426) hydrogen bonds : bond 0.03369 ( 637) hydrogen bonds : angle 3.58667 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1470.18 seconds wall clock time: 26 minutes 12.81 seconds (1572.81 seconds total)