Starting phenix.real_space_refine on Fri Jun 28 07:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt0_26106/06_2024/7tt0_26106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt0_26106/06_2024/7tt0_26106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt0_26106/06_2024/7tt0_26106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt0_26106/06_2024/7tt0_26106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt0_26106/06_2024/7tt0_26106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt0_26106/06_2024/7tt0_26106.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.056 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 4820 2.51 5 N 1297 2.21 5 O 1488 1.98 5 H 7253 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 14884 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 9052 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 5 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "P" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 386 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain breaks: 1 Time building chain proxies: 6.93, per 1000 atoms: 0.47 Number of scatterers: 14884 At special positions: 0 Unit cell: (107.382, 127.785, 104.161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 1488 8.00 N 1297 7.00 C 4820 6.00 H 7253 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino 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: 10.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 33.5% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 189 through 197 removed outlier: 4.594A pdb=" N ILE A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.742A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.886A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.937A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.504A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.671A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.061A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.599A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.929A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276 removed outlier: 5.878A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 355 removed outlier: 5.892A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.449A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.365A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG P1269 " --> pdb=" O VAL P1272 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE P1274 " --> pdb=" O GLU P1267 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU P1267 " --> pdb=" O PHE P1274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.327A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.955A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.946A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1098 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: 4.94 Time building geometry restraints manager: 10.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7253 1.03 - 1.23: 177 1.23 - 1.43: 3294 1.43 - 1.63: 4290 1.63 - 1.83: 48 Bond restraints: 15062 Sorted by residual: bond pdb=" CG ARG D 173 " pdb=" CD ARG D 173 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA LEU D 87 " pdb=" C LEU D 87 " ideal model delta sigma weight residual 1.522 1.506 0.015 1.40e-02 5.10e+03 1.22e+00 bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.16e+00 bond pdb=" CB TRP A 576 " pdb=" CG TRP A 576 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.11e+00 bond pdb=" CA MET D 218 " pdb=" C MET D 218 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.32e-02 5.74e+03 9.75e-01 ... (remaining 15057 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.73: 262 106.73 - 113.55: 16997 113.55 - 120.36: 5385 120.36 - 127.18: 4281 127.18 - 133.99: 82 Bond angle restraints: 27007 Sorted by residual: angle pdb=" N ASP A 332 " pdb=" CA ASP A 332 " pdb=" C ASP A 332 " ideal model delta sigma weight residual 108.76 100.46 8.30 1.69e+00 3.50e-01 2.41e+01 angle pdb=" N GLY A 431 " pdb=" CA GLY A 431 " pdb=" C GLY A 431 " ideal model delta sigma weight residual 111.62 104.90 6.72 1.77e+00 3.19e-01 1.44e+01 angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.76 103.65 6.11 1.64e+00 3.72e-01 1.39e+01 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 111.58 108.21 3.37 1.06e+00 8.90e-01 1.01e+01 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 111.82 108.26 3.56 1.16e+00 7.43e-01 9.41e+00 ... (remaining 27002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 6805 17.27 - 34.54: 217 34.54 - 51.80: 116 51.80 - 69.07: 45 69.07 - 86.34: 8 Dihedral angle restraints: 7191 sinusoidal: 3829 harmonic: 3362 Sorted by residual: dihedral pdb=" CB GLU A 283 " pdb=" CG GLU A 283 " pdb=" CD GLU A 283 " pdb=" OE1 GLU A 283 " ideal model delta sinusoidal sigma weight residual 0.00 83.98 -83.98 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CA ALA C 52 " pdb=" C ALA C 52 " pdb=" N PRO C 53 " pdb=" CA PRO C 53 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" CB GLU E 84 " pdb=" CG GLU E 84 " pdb=" CD GLU E 84 " pdb=" OE1 GLU E 84 " ideal model delta sinusoidal sigma weight residual 0.00 -81.29 81.29 1 3.00e+01 1.11e-03 9.05e+00 ... (remaining 7188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 756 0.040 - 0.079: 248 0.079 - 0.119: 82 0.119 - 0.158: 27 0.158 - 0.198: 2 Chirality restraints: 1115 Sorted by residual: chirality pdb=" CA TYR A 585 " pdb=" N TYR A 585 " pdb=" C TYR A 585 " pdb=" CB TYR A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ARG A 366 " pdb=" N ARG A 366 " pdb=" C ARG A 366 " pdb=" CB ARG A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1112 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PRO D 86 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO D 86 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU D 87 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 325 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C MET A 325 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 325 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO A 326 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 33 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C ASN D 33 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN D 33 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU D 34 " 0.014 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 505 2.16 - 2.77: 28627 2.77 - 3.38: 38432 3.38 - 3.99: 50343 3.99 - 4.60: 78570 Nonbonded interactions: 196477 Sorted by model distance: nonbonded pdb=" OE1 GLN A 445 " pdb=" HZ2 LYS A 808 " model vdw 1.552 1.850 nonbonded pdb=" OD1 ASP E 31 " pdb=" H GLY E 82 " model vdw 1.555 1.850 nonbonded pdb=" HG SER A 715 " pdb=" OD1 ASP A 740 " model vdw 1.566 1.850 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.569 1.850 nonbonded pdb="HE22 GLN E 34 " pdb=" O GLY D 189 " model vdw 1.588 1.850 ... (remaining 196472 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 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: 0.680 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: 0.230 Extract box with map and model: 3.210 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 45.080 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7809 Z= 0.298 Angle : 0.836 8.296 10595 Z= 0.527 Chirality : 0.046 0.198 1115 Planarity : 0.005 0.035 1402 Dihedral : 10.421 86.340 2832 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 1.30 (0.26), residues: 940 helix: 0.80 (0.28), residues: 273 sheet: 1.04 (0.30), residues: 276 loop : 1.01 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.031 0.002 PHE A 586 TYR 0.024 0.003 TYR A 468 ARG 0.025 0.003 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8933 (m-80) cc_final: 0.8584 (m-80) REVERT: A 322 VAL cc_start: 0.8610 (t) cc_final: 0.8064 (p) REVERT: A 401 ASP cc_start: 0.8220 (t0) cc_final: 0.7999 (t0) REVERT: A 449 TRP cc_start: 0.8276 (t60) cc_final: 0.8027 (t60) REVERT: A 450 LEU cc_start: 0.9072 (mt) cc_final: 0.8817 (mt) REVERT: A 731 ASN cc_start: 0.9218 (m-40) cc_final: 0.8948 (t0) REVERT: E 26 VAL cc_start: 0.9440 (m) cc_final: 0.9216 (p) REVERT: E 91 LEU cc_start: 0.9170 (tp) cc_final: 0.8859 (tp) REVERT: E 94 THR cc_start: 0.9069 (m) cc_final: 0.8851 (p) REVERT: E 101 LEU cc_start: 0.8797 (tp) cc_final: 0.8466 (tp) REVERT: E 103 ASN cc_start: 0.8319 (t0) cc_final: 0.8015 (t0) REVERT: D 127 PHE cc_start: 0.8758 (t80) cc_final: 0.8290 (t80) REVERT: D 227 MET cc_start: 0.8430 (mtt) cc_final: 0.8080 (mtt) REVERT: D 234 VAL cc_start: 0.9166 (t) cc_final: 0.8882 (p) REVERT: C 81 ASP cc_start: 0.8211 (t0) cc_final: 0.7489 (t0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.4417 time to fit residues: 178.6856 Evaluate side-chains 193 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0020 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN A 651 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7809 Z= 0.165 Angle : 0.524 4.119 10595 Z= 0.295 Chirality : 0.042 0.154 1115 Planarity : 0.004 0.042 1402 Dihedral : 4.947 76.157 1066 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.77 (0.27), residues: 940 helix: 2.23 (0.31), residues: 275 sheet: 0.74 (0.30), residues: 281 loop : 0.90 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 546 HIS 0.004 0.001 HIS A 533 PHE 0.016 0.001 PHE A 586 TYR 0.018 0.001 TYR C 41 ARG 0.006 0.001 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9017 (m-80) cc_final: 0.8534 (m-80) REVERT: A 449 TRP cc_start: 0.8451 (t60) cc_final: 0.7979 (t60) REVERT: A 450 LEU cc_start: 0.9045 (mt) cc_final: 0.8835 (mt) REVERT: A 609 TYR cc_start: 0.8839 (p90) cc_final: 0.8574 (p90) REVERT: E 26 VAL cc_start: 0.9483 (m) cc_final: 0.9222 (p) REVERT: E 66 ASP cc_start: 0.8275 (t0) cc_final: 0.7968 (t0) REVERT: E 91 LEU cc_start: 0.9011 (tp) cc_final: 0.8807 (tp) REVERT: E 94 THR cc_start: 0.9278 (m) cc_final: 0.9060 (p) REVERT: E 103 ASN cc_start: 0.8378 (t0) cc_final: 0.7612 (m110) REVERT: D 75 LEU cc_start: 0.8947 (mt) cc_final: 0.8648 (mt) REVERT: D 82 ASN cc_start: 0.8591 (t0) cc_final: 0.8321 (t0) REVERT: D 109 MET cc_start: 0.8796 (mtt) cc_final: 0.8440 (mmt) REVERT: D 127 PHE cc_start: 0.8723 (t80) cc_final: 0.8244 (t80) REVERT: D 154 TYR cc_start: 0.7993 (m-80) cc_final: 0.7691 (m-80) REVERT: D 227 MET cc_start: 0.8027 (mtt) cc_final: 0.7804 (mmm) REVERT: D 234 VAL cc_start: 0.9155 (t) cc_final: 0.8881 (p) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3527 time to fit residues: 110.0496 Evaluate side-chains 176 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 651 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7809 Z= 0.145 Angle : 0.469 3.904 10595 Z= 0.260 Chirality : 0.041 0.147 1115 Planarity : 0.004 0.044 1402 Dihedral : 4.775 77.380 1066 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 1.76 (0.27), residues: 940 helix: 2.44 (0.31), residues: 276 sheet: 0.58 (0.30), residues: 281 loop : 0.84 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.004 0.001 HIS A 533 PHE 0.011 0.001 PHE A 738 TYR 0.012 0.001 TYR C 41 ARG 0.003 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8270 (m-80) cc_final: 0.7797 (m-10) REVERT: A 449 TRP cc_start: 0.8313 (t60) cc_final: 0.7925 (t60) REVERT: E 66 ASP cc_start: 0.8300 (t0) cc_final: 0.7931 (t0) REVERT: E 91 LEU cc_start: 0.9125 (tp) cc_final: 0.8894 (tp) REVERT: E 94 THR cc_start: 0.9301 (m) cc_final: 0.9087 (p) REVERT: E 103 ASN cc_start: 0.8417 (t0) cc_final: 0.7677 (m110) REVERT: D 82 ASN cc_start: 0.8558 (t0) cc_final: 0.8303 (t0) REVERT: D 227 MET cc_start: 0.8228 (mtt) cc_final: 0.7968 (mmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3381 time to fit residues: 102.0104 Evaluate side-chains 172 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7809 Z= 0.247 Angle : 0.499 6.702 10595 Z= 0.279 Chirality : 0.040 0.143 1115 Planarity : 0.004 0.047 1402 Dihedral : 4.900 83.661 1066 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 1.30 (0.27), residues: 940 helix: 2.07 (0.30), residues: 276 sheet: 0.34 (0.30), residues: 279 loop : 0.53 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 576 HIS 0.004 0.001 HIS A 533 PHE 0.011 0.001 PHE A 648 TYR 0.014 0.001 TYR D 184 ARG 0.003 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8391 (m-80) cc_final: 0.7938 (m-10) REVERT: A 449 TRP cc_start: 0.8358 (t60) cc_final: 0.7963 (t60) REVERT: A 545 MET cc_start: 0.9431 (mmm) cc_final: 0.9218 (mmm) REVERT: A 701 LYS cc_start: 0.8953 (tttt) cc_final: 0.8582 (ttmm) REVERT: E 26 VAL cc_start: 0.9453 (t) cc_final: 0.9201 (p) REVERT: D 82 ASN cc_start: 0.8589 (t0) cc_final: 0.8329 (t0) REVERT: D 127 PHE cc_start: 0.8736 (t80) cc_final: 0.8300 (t80) REVERT: D 227 MET cc_start: 0.8272 (mtt) cc_final: 0.7992 (mmm) REVERT: C 81 ASP cc_start: 0.7931 (t0) cc_final: 0.7706 (t0) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3488 time to fit residues: 95.3969 Evaluate side-chains 164 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7809 Z= 0.173 Angle : 0.461 3.710 10595 Z= 0.255 Chirality : 0.040 0.142 1115 Planarity : 0.004 0.044 1402 Dihedral : 4.864 86.379 1066 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 1.34 (0.27), residues: 940 helix: 2.18 (0.30), residues: 277 sheet: 0.45 (0.30), residues: 274 loop : 0.40 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.026 0.001 PHE A 785 TYR 0.021 0.001 TYR A 550 ARG 0.002 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8397 (m-80) cc_final: 0.7931 (m-10) REVERT: A 449 TRP cc_start: 0.8317 (t60) cc_final: 0.7923 (t60) REVERT: A 508 SER cc_start: 0.7616 (p) cc_final: 0.7261 (m) REVERT: A 545 MET cc_start: 0.9127 (mmm) cc_final: 0.8925 (mmm) REVERT: A 701 LYS cc_start: 0.8942 (tttt) cc_final: 0.8584 (ttmm) REVERT: E 26 VAL cc_start: 0.9441 (t) cc_final: 0.9177 (p) REVERT: D 82 ASN cc_start: 0.8609 (t0) cc_final: 0.8353 (t0) REVERT: D 127 PHE cc_start: 0.8727 (t80) cc_final: 0.8307 (t80) REVERT: D 227 MET cc_start: 0.8005 (mtt) cc_final: 0.7772 (mmm) REVERT: C 81 ASP cc_start: 0.8132 (t0) cc_final: 0.7832 (t0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3398 time to fit residues: 90.7082 Evaluate side-chains 167 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7809 Z= 0.208 Angle : 0.474 5.148 10595 Z= 0.261 Chirality : 0.040 0.146 1115 Planarity : 0.006 0.122 1402 Dihedral : 4.945 89.164 1066 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 1.13 (0.27), residues: 940 helix: 2.01 (0.30), residues: 277 sheet: 0.24 (0.30), residues: 278 loop : 0.35 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.024 0.001 PHE A 785 TYR 0.014 0.001 TYR D 184 ARG 0.013 0.001 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8434 (m-80) cc_final: 0.7985 (m-10) REVERT: A 408 SER cc_start: 0.9000 (t) cc_final: 0.8390 (m) REVERT: A 449 TRP cc_start: 0.8320 (t60) cc_final: 0.7942 (t60) REVERT: A 508 SER cc_start: 0.7687 (p) cc_final: 0.7317 (m) REVERT: A 701 LYS cc_start: 0.8938 (tttt) cc_final: 0.8590 (ttmm) REVERT: E 26 VAL cc_start: 0.9453 (t) cc_final: 0.9194 (p) REVERT: D 82 ASN cc_start: 0.8582 (t0) cc_final: 0.8341 (t0) REVERT: D 127 PHE cc_start: 0.8749 (t80) cc_final: 0.8322 (t80) REVERT: D 227 MET cc_start: 0.8049 (mtt) cc_final: 0.7729 (mmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3311 time to fit residues: 89.6856 Evaluate side-chains 163 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 7809 Z= 0.328 Angle : 0.532 4.843 10595 Z= 0.299 Chirality : 0.042 0.391 1115 Planarity : 0.005 0.046 1402 Dihedral : 4.894 78.732 1066 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % Cbeta Deviations : 0.11 % 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: 0.68 (0.27), residues: 940 helix: 1.63 (0.30), residues: 277 sheet: -0.04 (0.30), residues: 279 loop : 0.12 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.003 0.001 HIS A 280 PHE 0.012 0.001 PHE E 77 TYR 0.016 0.002 TYR D 184 ARG 0.005 0.001 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8458 (m-80) cc_final: 0.8038 (m-10) REVERT: A 408 SER cc_start: 0.9028 (t) cc_final: 0.8418 (m) REVERT: A 422 ASN cc_start: 0.8441 (m-40) cc_final: 0.8081 (m-40) REVERT: A 449 TRP cc_start: 0.8309 (t60) cc_final: 0.7972 (t60) REVERT: A 609 TYR cc_start: 0.8790 (p90) cc_final: 0.8579 (p90) REVERT: A 701 LYS cc_start: 0.8943 (tttt) cc_final: 0.8605 (ttmm) REVERT: E 26 VAL cc_start: 0.9498 (t) cc_final: 0.9251 (p) REVERT: D 82 ASN cc_start: 0.8627 (t0) cc_final: 0.8327 (t0) REVERT: D 127 PHE cc_start: 0.8766 (t80) cc_final: 0.8346 (t80) REVERT: D 227 MET cc_start: 0.8121 (mtt) cc_final: 0.7810 (mmm) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.3461 time to fit residues: 90.7141 Evaluate side-chains 161 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7809 Z= 0.150 Angle : 0.470 5.107 10595 Z= 0.257 Chirality : 0.042 0.342 1115 Planarity : 0.004 0.041 1402 Dihedral : 4.676 66.949 1066 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.70 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.98 (0.28), residues: 940 helix: 2.07 (0.31), residues: 277 sheet: -0.00 (0.29), residues: 278 loop : 0.24 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 739 HIS 0.003 0.000 HIS D 102 PHE 0.013 0.001 PHE A 426 TYR 0.012 0.001 TYR D 184 ARG 0.003 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8420 (m-80) cc_final: 0.7994 (m-10) REVERT: A 408 SER cc_start: 0.9031 (t) cc_final: 0.8411 (m) REVERT: A 422 ASN cc_start: 0.8375 (m-40) cc_final: 0.7983 (m-40) REVERT: A 449 TRP cc_start: 0.8205 (t60) cc_final: 0.7848 (t60) REVERT: A 508 SER cc_start: 0.7606 (p) cc_final: 0.7240 (m) REVERT: A 701 LYS cc_start: 0.8914 (tttt) cc_final: 0.8602 (ttmm) REVERT: E 26 VAL cc_start: 0.9532 (t) cc_final: 0.9275 (p) REVERT: D 82 ASN cc_start: 0.8612 (t0) cc_final: 0.8324 (t0) REVERT: D 127 PHE cc_start: 0.8739 (t80) cc_final: 0.8332 (t80) REVERT: D 227 MET cc_start: 0.7989 (mtt) cc_final: 0.7732 (mmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3289 time to fit residues: 87.4186 Evaluate side-chains 161 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7809 Z= 0.272 Angle : 0.521 5.384 10595 Z= 0.292 Chirality : 0.042 0.366 1115 Planarity : 0.004 0.044 1402 Dihedral : 4.728 53.539 1066 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.53 (0.27), residues: 940 helix: 1.69 (0.30), residues: 276 sheet: -0.27 (0.30), residues: 278 loop : -0.00 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 739 HIS 0.004 0.001 HIS A 280 PHE 0.012 0.002 PHE E 77 TYR 0.017 0.001 TYR A 468 ARG 0.005 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8465 (m-80) cc_final: 0.8055 (m-10) REVERT: A 408 SER cc_start: 0.9049 (t) cc_final: 0.8332 (m) REVERT: A 422 ASN cc_start: 0.8283 (m-40) cc_final: 0.7845 (m-40) REVERT: A 449 TRP cc_start: 0.8266 (t60) cc_final: 0.7994 (t60) REVERT: A 701 LYS cc_start: 0.8921 (tttt) cc_final: 0.8607 (ttmm) REVERT: E 26 VAL cc_start: 0.9544 (t) cc_final: 0.9293 (p) REVERT: D 82 ASN cc_start: 0.8541 (t0) cc_final: 0.8271 (t0) REVERT: D 127 PHE cc_start: 0.8786 (t80) cc_final: 0.8375 (t80) REVERT: D 227 MET cc_start: 0.8146 (mtt) cc_final: 0.7899 (mmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3369 time to fit residues: 85.8066 Evaluate side-chains 157 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7809 Z= 0.181 Angle : 0.496 7.941 10595 Z= 0.274 Chirality : 0.043 0.375 1115 Planarity : 0.004 0.046 1402 Dihedral : 4.686 49.789 1066 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.58 (0.27), residues: 940 helix: 1.80 (0.30), residues: 277 sheet: -0.29 (0.30), residues: 280 loop : 0.02 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 739 HIS 0.002 0.000 HIS A 280 PHE 0.010 0.001 PHE E 77 TYR 0.015 0.001 TYR D 184 ARG 0.009 0.000 ARG D 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8454 (m-80) cc_final: 0.8040 (m-10) REVERT: A 408 SER cc_start: 0.9008 (t) cc_final: 0.8378 (m) REVERT: A 422 ASN cc_start: 0.8426 (m-40) cc_final: 0.7948 (m-40) REVERT: A 449 TRP cc_start: 0.8207 (t60) cc_final: 0.7942 (t60) REVERT: A 508 SER cc_start: 0.7655 (p) cc_final: 0.7265 (m) REVERT: A 701 LYS cc_start: 0.8887 (tttt) cc_final: 0.8594 (ttmm) REVERT: E 26 VAL cc_start: 0.9535 (t) cc_final: 0.9291 (p) REVERT: D 60 ASN cc_start: 0.9077 (m110) cc_final: 0.8829 (m110) REVERT: D 82 ASN cc_start: 0.8483 (t0) cc_final: 0.8234 (t0) REVERT: D 127 PHE cc_start: 0.8776 (t80) cc_final: 0.8360 (t80) REVERT: D 227 MET cc_start: 0.8085 (mtt) cc_final: 0.7825 (mmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3579 time to fit residues: 90.5802 Evaluate side-chains 157 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096121 restraints weight = 46147.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100808 restraints weight = 21785.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103519 restraints weight = 14376.260| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7809 Z= 0.143 Angle : 0.470 5.630 10595 Z= 0.257 Chirality : 0.042 0.333 1115 Planarity : 0.004 0.049 1402 Dihedral : 4.511 47.518 1066 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.74 (0.28), residues: 940 helix: 2.10 (0.30), residues: 277 sheet: -0.25 (0.30), residues: 279 loop : -0.00 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 739 HIS 0.002 0.000 HIS A 533 PHE 0.009 0.001 PHE A 738 TYR 0.013 0.001 TYR D 184 ARG 0.006 0.000 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.40 seconds wall clock time: 63 minutes 37.29 seconds (3817.29 seconds total)