Starting phenix.real_space_refine (version: 1.20rc4) on Thu Dec 2 00:52:38 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kar_22781/12_2021/7kar_22781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kar_22781/12_2021/7kar_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kar_22781/12_2021/7kar_22781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kar_22781/12_2021/7kar_22781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kar_22781/12_2021/7kar_22781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kar_22781/12_2021/7kar_22781.pdb" } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: 5.92, per 1000 atoms: 0.57 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 - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 1.6 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: 0.46 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: 2.78 Time building geometry restraints manager: 4.70 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: 100.08 - 106.86: 300 106.86 - 113.65: 6121 113.65 - 120.43: 4203 120.43 - 127.22: 3694 127.22 - 134.00: 108 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 2.440 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.234 2.520 nonbonded pdb=" O SER A 444 " pdb=" OG SER A 447 " model vdw 2.264 2.440 nonbonded pdb=" NZ LYS A 273 " pdb=" O GLN A 398 " model vdw 2.281 2.520 nonbonded pdb=" ND2 ASN D 55 " pdb=" O LEU D 496 " model vdw 2.281 2.520 ... (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 ========== 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 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. 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 28.610 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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= 0.217 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.153 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 outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2372 time to fit residues: 37.1631 Evaluate side-chains 62 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7022 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 403 ASN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS D 427 ASN D 494 GLN E 88 HIS E 123 ASN ** 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 ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 10643 Z= 0.297 Angle : 0.634 12.514 14426 Z= 0.315 Chirality : 0.041 0.156 1710 Planarity : 0.004 0.043 1793 Dihedral : 3.839 21.853 1422 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.00 (0.23), residues: 1317 helix: 1.24 (0.18), residues: 809 sheet: -2.48 (0.44), residues: 106 loop : -1.81 (0.30), residues: 402 *********************** 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 fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 85 average time/residue: 0.1801 time to fit residues: 24.7622 Evaluate side-chains 68 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0953 time to fit residues: 3.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 298 GLN D 494 GLN E 174 GLN F 68 ASN F 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10643 Z= 0.147 Angle : 0.547 9.981 14426 Z= 0.266 Chirality : 0.038 0.156 1710 Planarity : 0.003 0.045 1793 Dihedral : 3.583 19.706 1422 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.99 % 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: 0.84 (0.24), residues: 1317 helix: 1.81 (0.18), residues: 815 sheet: -1.83 (0.48), residues: 102 loop : -1.43 (0.31), residues: 400 *********************** 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 89 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 88 average time/residue: 0.1858 time to fit residues: 25.9363 Evaluate side-chains 68 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0947 time to fit residues: 2.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 120 optimal weight: 0.0570 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10643 Z= 0.200 Angle : 0.571 10.349 14426 Z= 0.279 Chirality : 0.039 0.150 1710 Planarity : 0.003 0.052 1793 Dihedral : 3.597 19.808 1422 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.72 % 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: 1.21 (0.24), residues: 1317 helix: 2.05 (0.19), residues: 814 sheet: -1.72 (0.49), residues: 104 loop : -1.13 (0.32), residues: 399 *********************** 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 80 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 77 average time/residue: 0.1767 time to fit residues: 21.9171 Evaluate side-chains 72 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0835 time to fit residues: 2.0940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10643 Z= 0.176 Angle : 0.558 10.999 14426 Z= 0.271 Chirality : 0.039 0.142 1710 Planarity : 0.003 0.054 1793 Dihedral : 3.536 18.559 1422 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.35 % 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: 1.45 (0.24), residues: 1317 helix: 2.17 (0.19), residues: 816 sheet: -1.42 (0.53), residues: 98 loop : -0.97 (0.32), residues: 403 *********************** 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 86 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 84 average time/residue: 0.1320 time to fit residues: 18.0702 Evaluate side-chains 71 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0932 time to fit residues: 2.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 GLN D 416 ASN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10643 Z= 0.205 Angle : 0.584 11.715 14426 Z= 0.282 Chirality : 0.039 0.139 1710 Planarity : 0.003 0.054 1793 Dihedral : 3.586 18.742 1422 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.90 % 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: 1.54 (0.25), residues: 1317 helix: 2.21 (0.19), residues: 812 sheet: -1.30 (0.55), residues: 98 loop : -0.85 (0.32), residues: 407 *********************** 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 84 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 81 average time/residue: 0.1743 time to fit residues: 23.1658 Evaluate side-chains 72 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1035 time to fit residues: 2.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 GLN D 416 ASN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10643 Z= 0.154 Angle : 0.579 12.909 14426 Z= 0.273 Chirality : 0.038 0.139 1710 Planarity : 0.003 0.053 1793 Dihedral : 3.449 18.424 1422 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.90 % 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: 1.69 (0.25), residues: 1317 helix: 2.28 (0.19), residues: 818 sheet: -1.09 (0.55), residues: 96 loop : -0.76 (0.32), residues: 403 *********************** 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 88 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 87 average time/residue: 0.1894 time to fit residues: 26.3574 Evaluate side-chains 77 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1107 time to fit residues: 2.5289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.0020 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS D 334 HIS D 412 GLN D 416 ASN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2595 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= 0.167 Angle : 0.592 12.465 14426 Z= 0.280 Chirality : 0.038 0.138 1710 Planarity : 0.003 0.053 1793 Dihedral : 3.465 18.564 1422 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.45 % 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: 1.74 (0.25), residues: 1317 helix: 2.27 (0.19), residues: 820 sheet: -1.00 (0.55), residues: 96 loop : -0.65 (0.33), residues: 401 *********************** 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 80 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.1842 time to fit residues: 22.4794 Evaluate side-chains 75 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0871 time to fit residues: 1.8627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 GLN D 416 ASN D 520 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2684 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= 0.180 Angle : 0.606 13.111 14426 Z= 0.286 Chirality : 0.039 0.139 1710 Planarity : 0.003 0.053 1793 Dihedral : 3.485 18.395 1422 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.54 % 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: 1.69 (0.25), residues: 1317 helix: 2.16 (0.19), residues: 828 sheet: -0.93 (0.56), residues: 96 loop : -0.58 (0.33), residues: 393 *********************** 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 fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.1778 time to fit residues: 23.1348 Evaluate side-chains 75 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1128 time to fit residues: 2.4024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 GLN D 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 10643 Z= 0.306 Angle : 0.673 14.271 14426 Z= 0.326 Chirality : 0.041 0.144 1710 Planarity : 0.004 0.056 1793 Dihedral : 3.778 18.764 1422 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.72 % 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: 1.52 (0.24), residues: 1317 helix: 2.01 (0.19), residues: 823 sheet: -1.06 (0.56), residues: 98 loop : -0.54 (0.33), residues: 396 ********************** 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 79 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1819 time to fit residues: 22.0518 Evaluate side-chains 71 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1106 time to fit residues: 2.4953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 GLN D 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047704 restraints weight = 59955.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048258 restraints weight = 38207.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048513 restraints weight = 27848.178| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10643 Z= 0.155 Angle : 0.603 13.222 14426 Z= 0.286 Chirality : 0.039 0.139 1710 Planarity : 0.003 0.051 1793 Dihedral : 3.546 18.774 1422 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.00 % 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: 1.79 (0.25), residues: 1317 helix: 2.19 (0.19), residues: 829 sheet: -0.83 (0.57), residues: 96 loop : -0.46 (0.33), residues: 392 =============================================================================== Job complete usr+sys time: 1493.62 seconds wall clock time: 29 minutes 23.86 seconds (1763.86 seconds total)