Starting phenix.real_space_refine on Fri Mar 15 08:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyu_30018/03_2024/6lyu_30018.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyu_30018/03_2024/6lyu_30018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyu_30018/03_2024/6lyu_30018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyu_30018/03_2024/6lyu_30018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyu_30018/03_2024/6lyu_30018.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyu_30018/03_2024/6lyu_30018.pdb" } resolution = 4.2 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= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 7001 2.51 5 N 1896 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11118 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5567 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2762 Classifications: {'peptide': 367} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 353} Chain: "C" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 343 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 5, 'TRANS': 42} Chain breaks: 1 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Time building chain proxies: 6.13, per 1000 atoms: 0.55 Number of scatterers: 11118 At special positions: 0 Unit cell: (134, 100, 131, 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 31 16.00 O 2190 8.00 N 1896 7.00 C 7001 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 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: 4.95 Conformation dependent library (CDL) restraints added in 2.2 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 21 sheets defined 24.2% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.589A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.366A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.864A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.500A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.565A 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 553 Processing helix chain 'A' and resid 640 through 644 removed outlier: 3.690A pdb=" N GLY A 643 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.906A pdb=" N TYR A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 59 through 63 removed outlier: 4.318A pdb=" N SER C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 65 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.875A pdb=" N PHE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.961A pdb=" N ALA D 163 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 46 removed outlier: 4.038A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.614A pdb=" N ASP A 164 " --> pdb=" O THR A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 182 removed outlier: 6.416A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLN A 178 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 12.771A pdb=" N VAL A 258 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N ILE A 180 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 12.270A pdb=" N ILE A 260 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N ILE A 182 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR A 261 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 239 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 275 removed outlier: 4.262A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.670A pdb=" N ASP A 401 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 430 removed outlier: 4.126A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 458 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 491 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 430 removed outlier: 4.126A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 458 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 491 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 528 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 532 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AA9, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.767A pdb=" N LEU A 613 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 634 " --> pdb=" O VAL A 713 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.236A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 768 through 771 removed outlier: 6.348A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 778 " --> pdb=" O GLY A 781 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 768 through 771 removed outlier: 6.348A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 786 " --> pdb=" O GLN A 803 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.519A pdb=" N ALA B 74 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.566A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.734A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 201 through 202 removed outlier: 3.708A pdb=" N VAL B 209 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 257 through 259 removed outlier: 6.426A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 291 through 292 removed outlier: 6.179A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 327 through 333 removed outlier: 5.506A pdb=" N SER B 329 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY B 340 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 345 through 346 removed outlier: 3.693A pdb=" N GLN B 360 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 73 through 77 removed outlier: 3.798A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3403 1.33 - 1.45: 1984 1.45 - 1.57: 5912 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 11360 Sorted by residual: bond pdb=" C ALA A 442 " pdb=" N GLY A 443 " ideal model delta sigma weight residual 1.330 1.564 -0.234 8.50e-03 1.38e+04 7.58e+02 bond pdb=" C GLN A 446 " pdb=" N ASP A 447 " ideal model delta sigma weight residual 1.332 1.458 -0.126 1.40e-02 5.10e+03 8.07e+01 bond pdb=" CA SER A 439 " pdb=" CB SER A 439 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.69e-02 3.50e+03 1.39e+01 bond pdb=" C THR A 423 " pdb=" N GLY A 424 " ideal model delta sigma weight residual 1.331 1.382 -0.052 1.46e-02 4.69e+03 1.25e+01 bond pdb=" N THR A 434 " pdb=" CA THR A 434 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.19e+01 ... (remaining 11355 not shown) Histogram of bond angle deviations from ideal: 91.00 - 101.59: 27 101.59 - 112.18: 5760 112.18 - 122.77: 8395 122.77 - 133.36: 1238 133.36 - 143.95: 26 Bond angle restraints: 15446 Sorted by residual: angle pdb=" CA THR A 423 " pdb=" C THR A 423 " pdb=" N GLY A 424 " ideal model delta sigma weight residual 116.51 141.28 -24.77 1.34e+00 5.57e-01 3.42e+02 angle pdb=" O THR A 423 " pdb=" C THR A 423 " pdb=" N GLY A 424 " ideal model delta sigma weight residual 123.12 102.43 20.69 1.32e+00 5.74e-01 2.46e+02 angle pdb=" C THR A 423 " pdb=" N GLY A 424 " pdb=" CA GLY A 424 " ideal model delta sigma weight residual 121.41 143.95 -22.54 1.96e+00 2.60e-01 1.32e+02 angle pdb=" C ASN A 463 " pdb=" CA ASN A 463 " pdb=" CB ASN A 463 " ideal model delta sigma weight residual 109.80 93.71 16.09 1.70e+00 3.46e-01 8.95e+01 angle pdb=" N SER A 439 " pdb=" CA SER A 439 " pdb=" C SER A 439 " ideal model delta sigma weight residual 110.80 91.00 19.80 2.13e+00 2.20e-01 8.64e+01 ... (remaining 15441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5883 17.92 - 35.84: 692 35.84 - 53.76: 110 53.76 - 71.68: 14 71.68 - 89.60: 8 Dihedral angle restraints: 6707 sinusoidal: 2599 harmonic: 4108 Sorted by residual: dihedral pdb=" C ASN A 805 " pdb=" N ASN A 805 " pdb=" CA ASN A 805 " pdb=" CB ASN A 805 " ideal model delta harmonic sigma weight residual -122.60 -149.59 26.99 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N ASN A 805 " pdb=" C ASN A 805 " pdb=" CA ASN A 805 " pdb=" CB ASN A 805 " ideal model delta harmonic sigma weight residual 122.80 147.04 -24.24 0 2.50e+00 1.60e-01 9.40e+01 dihedral pdb=" CA THR B 386 " pdb=" C THR B 386 " pdb=" N VAL B 387 " pdb=" CA VAL B 387 " ideal model delta harmonic sigma weight residual -180.00 -140.63 -39.37 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 6704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 1677 0.201 - 0.402: 6 0.402 - 0.603: 2 0.603 - 0.804: 1 0.804 - 1.005: 1 Chirality restraints: 1687 Sorted by residual: chirality pdb=" CA ASN A 805 " pdb=" N ASN A 805 " pdb=" C ASN A 805 " pdb=" CB ASN A 805 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CA ASP A 464 " pdb=" N ASP A 464 " pdb=" C ASP A 464 " pdb=" CB ASP A 464 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA THR A 434 " pdb=" N THR A 434 " pdb=" C THR A 434 " pdb=" CB THR A 434 " both_signs ideal model delta sigma weight residual False 2.53 1.93 0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 1684 not shown) Planarity restraints: 2036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 421 " 0.958 9.50e-02 1.11e+02 4.30e-01 1.12e+02 pdb=" NE ARG A 421 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 421 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 421 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 421 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 420 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C GLU A 420 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU A 420 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG A 421 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 206 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C PRO D 206 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO D 206 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP D 207 " -0.016 2.00e-02 2.50e+03 ... (remaining 2033 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 390 2.57 - 3.15: 12152 3.15 - 3.73: 19956 3.73 - 4.32: 27248 4.32 - 4.90: 40176 Nonbonded interactions: 99922 Sorted by model distance: nonbonded pdb=" O ARG A 488 " pdb=" OG1 THR A 511 " model vdw 1.986 2.440 nonbonded pdb=" OH TYR D 184 " pdb=" NH2 ARG D 188 " model vdw 1.989 2.520 nonbonded pdb=" CA PHE A 395 " pdb=" CB GLU A 420 " model vdw 2.042 3.870 nonbonded pdb=" O ILE A 352 " pdb=" NH2 ARG A 366 " model vdw 2.053 2.520 nonbonded pdb=" O THR A 720 " pdb=" OG1 THR A 735 " model vdw 2.054 2.440 ... (remaining 99917 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.920 Check model and map are aligned: 0.180 Set scattering table: 0.090 Process input model: 33.830 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.009 0.234 11360 Z= 0.602 Angle : 1.165 24.767 15446 Z= 0.675 Chirality : 0.065 1.005 1687 Planarity : 0.011 0.430 2036 Dihedral : 15.383 89.604 4095 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 57.04 Ramachandran Plot: Outliers : 0.71 % Allowed : 23.09 % Favored : 76.20 % Rotamer: Outliers : 1.18 % Allowed : 12.75 % Favored : 86.06 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.59 % 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: -6.16 (0.17), residues: 1416 helix: -3.48 (0.19), residues: 288 sheet: -3.78 (0.23), residues: 356 loop : -4.65 (0.17), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 749 HIS 0.011 0.002 HIS E 83 PHE 0.028 0.003 PHE A 791 TYR 0.035 0.003 TYR B 73 ARG 0.016 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.370 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: A 177 ILE cc_start: 0.8648 (mt) cc_final: 0.8444 (mt) REVERT: A 395 PHE cc_start: 0.6928 (p90) cc_final: 0.6565 (p90) REVERT: A 396 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 425 SER cc_start: 0.6729 (OUTLIER) cc_final: 0.6189 (p) REVERT: A 552 MET cc_start: 0.8979 (mmm) cc_final: 0.8756 (mmp) REVERT: B 378 LEU cc_start: 0.9259 (tp) cc_final: 0.9051 (tp) REVERT: C 39 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8380 (mm-30) REVERT: D 34 GLU cc_start: 0.9662 (tp30) cc_final: 0.9354 (tp30) REVERT: D 53 THR cc_start: 0.8553 (p) cc_final: 0.8297 (p) REVERT: D 56 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8619 (tm-30) REVERT: D 165 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8394 (mmmt) REVERT: D 187 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8252 (mm-30) REVERT: D 232 GLU cc_start: 0.8604 (pm20) cc_final: 0.8363 (pm20) outliers start: 14 outliers final: 3 residues processed: 167 average time/residue: 0.2443 time to fit residues: 57.1310 Evaluate side-chains 122 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 20.0000 chunk 106 optimal weight: 0.0060 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 345 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 196 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11360 Z= 0.237 Angle : 0.790 13.170 15446 Z= 0.415 Chirality : 0.048 0.181 1687 Planarity : 0.005 0.080 2036 Dihedral : 7.201 40.514 1563 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.48 % Favored : 85.10 % Rotamer: Outliers : 0.17 % Allowed : 7.09 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.22 % 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: -4.72 (0.19), residues: 1416 helix: -1.52 (0.25), residues: 307 sheet: -3.12 (0.24), residues: 378 loop : -3.96 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 576 HIS 0.006 0.001 HIS E 83 PHE 0.023 0.002 PHE A 738 TYR 0.021 0.002 TYR A 618 ARG 0.010 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.347 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: A 251 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7305 (mppt) REVERT: A 545 MET cc_start: 0.9022 (mtt) cc_final: 0.8571 (mtt) REVERT: B 127 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8626 (mt-10) REVERT: D 97 ARG cc_start: 0.8985 (ptt90) cc_final: 0.8778 (ptt-90) REVERT: E 71 ASN cc_start: 0.7575 (t0) cc_final: 0.7029 (t0) REVERT: E 95 PHE cc_start: 0.8434 (m-80) cc_final: 0.7529 (m-80) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2431 time to fit residues: 64.7593 Evaluate side-chains 137 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 538 ASN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 266 ASN B 287 ASN B 301 GLN B 324 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11360 Z= 0.250 Angle : 0.731 11.352 15446 Z= 0.385 Chirality : 0.046 0.177 1687 Planarity : 0.005 0.047 2036 Dihedral : 6.852 39.375 1563 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.76 % Favored : 84.96 % Rotamer: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.22 % 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: -4.04 (0.21), residues: 1416 helix: -0.76 (0.27), residues: 309 sheet: -2.72 (0.26), residues: 369 loop : -3.63 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 546 HIS 0.006 0.001 HIS E 83 PHE 0.019 0.002 PHE A 738 TYR 0.029 0.002 TYR A 618 ARG 0.008 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 1.339 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: A 303 LYS cc_start: 0.8823 (tmmt) cc_final: 0.8604 (tmtt) REVERT: A 368 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7118 (tp30) REVERT: A 711 MET cc_start: 0.8826 (ttt) cc_final: 0.8568 (ttm) REVERT: C 34 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 149 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8505 (tmmt) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.2461 time to fit residues: 56.2327 Evaluate side-chains 129 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11360 Z= 0.197 Angle : 0.685 10.181 15446 Z= 0.357 Chirality : 0.045 0.157 1687 Planarity : 0.004 0.051 2036 Dihedral : 6.419 39.129 1563 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.43 % Favored : 87.36 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.15 % 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: -3.45 (0.21), residues: 1416 helix: -0.17 (0.28), residues: 308 sheet: -2.43 (0.26), residues: 365 loop : -3.25 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 103 HIS 0.004 0.001 HIS E 83 PHE 0.020 0.002 PHE D 128 TYR 0.027 0.002 TYR B 263 ARG 0.005 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.9489 (mm) cc_final: 0.9277 (mp) REVERT: A 303 LYS cc_start: 0.8800 (tmmt) cc_final: 0.8514 (tmtt) REVERT: A 321 ARG cc_start: 0.7850 (tpm170) cc_final: 0.7608 (tpm170) REVERT: A 368 GLU cc_start: 0.7998 (mm-30) cc_final: 0.6882 (tp30) REVERT: A 396 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 618 TYR cc_start: 0.8847 (m-10) cc_final: 0.8635 (m-10) REVERT: A 711 MET cc_start: 0.8624 (ttt) cc_final: 0.8342 (ttm) REVERT: D 58 LEU cc_start: 0.8613 (tp) cc_final: 0.8378 (tp) REVERT: D 169 PHE cc_start: 0.8159 (t80) cc_final: 0.7932 (t80) REVERT: E 46 ILE cc_start: 0.7698 (mm) cc_final: 0.7210 (mm) REVERT: E 50 MET cc_start: 0.7614 (ptp) cc_final: 0.6651 (ptp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2378 time to fit residues: 59.4408 Evaluate side-chains 131 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 44 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11360 Z= 0.256 Angle : 0.718 10.696 15446 Z= 0.375 Chirality : 0.044 0.160 1687 Planarity : 0.005 0.063 2036 Dihedral : 6.385 39.040 1563 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.70 % Favored : 86.09 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.43 (0.21), residues: 1416 helix: -0.29 (0.28), residues: 309 sheet: -2.27 (0.27), residues: 357 loop : -3.25 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 546 HIS 0.005 0.001 HIS E 83 PHE 0.047 0.002 PHE D 128 TYR 0.018 0.002 TYR C 65 ARG 0.014 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8774 (tmmt) cc_final: 0.8496 (tmtt) REVERT: A 368 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7181 (tp30) REVERT: A 396 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 618 TYR cc_start: 0.8871 (m-10) cc_final: 0.8626 (m-10) REVERT: A 648 PHE cc_start: 0.7565 (p90) cc_final: 0.7188 (p90) REVERT: D 34 GLU cc_start: 0.9567 (tp30) cc_final: 0.9277 (tp30) REVERT: E 46 ILE cc_start: 0.7594 (mm) cc_final: 0.7175 (mm) REVERT: E 71 ASN cc_start: 0.7465 (t0) cc_final: 0.6943 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2128 time to fit residues: 48.3222 Evaluate side-chains 126 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11360 Z= 0.240 Angle : 0.699 10.838 15446 Z= 0.366 Chirality : 0.044 0.156 1687 Planarity : 0.005 0.063 2036 Dihedral : 6.324 38.462 1563 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.12 % Favored : 85.73 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.29 (0.21), residues: 1416 helix: -0.04 (0.29), residues: 308 sheet: -2.21 (0.27), residues: 357 loop : -3.21 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 776 HIS 0.004 0.001 HIS D 139 PHE 0.034 0.002 PHE D 128 TYR 0.017 0.002 TYR D 79 ARG 0.012 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.351 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: A 303 LYS cc_start: 0.8767 (tmmt) cc_final: 0.8504 (tmtt) REVERT: A 368 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7063 (tp30) REVERT: A 618 TYR cc_start: 0.8931 (m-10) cc_final: 0.8669 (m-10) REVERT: A 648 PHE cc_start: 0.7486 (p90) cc_final: 0.6996 (p90) REVERT: A 711 MET cc_start: 0.8777 (ttt) cc_final: 0.8523 (ttm) REVERT: B 298 LEU cc_start: 0.8719 (pt) cc_final: 0.8486 (pt) REVERT: D 34 GLU cc_start: 0.9596 (tp30) cc_final: 0.9315 (tp30) REVERT: D 169 PHE cc_start: 0.7946 (t80) cc_final: 0.7601 (t80) REVERT: E 46 ILE cc_start: 0.7615 (mm) cc_final: 0.7230 (mm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2181 time to fit residues: 50.0222 Evaluate side-chains 127 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 748 ASN A 765 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11360 Z= 0.181 Angle : 0.659 9.386 15446 Z= 0.342 Chirality : 0.044 0.157 1687 Planarity : 0.005 0.068 2036 Dihedral : 5.976 38.187 1563 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.58 % Favored : 88.28 % Rotamer: Outliers : 0.08 % Allowed : 1.69 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.93 (0.22), residues: 1416 helix: 0.20 (0.28), residues: 309 sheet: -1.94 (0.27), residues: 357 loop : -2.99 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 776 HIS 0.005 0.001 HIS D 139 PHE 0.026 0.002 PHE D 128 TYR 0.020 0.001 TYR A 754 ARG 0.006 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8760 (tmmt) cc_final: 0.8479 (tmtt) REVERT: A 368 GLU cc_start: 0.8102 (mm-30) cc_final: 0.6890 (tp30) REVERT: A 396 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 618 TYR cc_start: 0.8957 (m-10) cc_final: 0.8728 (m-10) REVERT: A 648 PHE cc_start: 0.7478 (p90) cc_final: 0.6881 (p90) REVERT: A 711 MET cc_start: 0.8717 (ttt) cc_final: 0.8418 (ttm) REVERT: B 298 LEU cc_start: 0.8600 (pt) cc_final: 0.8358 (pt) REVERT: C 56 MET cc_start: 0.6987 (mpp) cc_final: 0.6455 (mpp) REVERT: C 83 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8226 (mmm160) REVERT: D 34 GLU cc_start: 0.9608 (tp30) cc_final: 0.9330 (tp30) REVERT: D 165 LYS cc_start: 0.8535 (pttp) cc_final: 0.8074 (pttp) REVERT: D 169 PHE cc_start: 0.7826 (t80) cc_final: 0.7536 (t80) REVERT: E 46 ILE cc_start: 0.7495 (mm) cc_final: 0.7164 (mm) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2227 time to fit residues: 54.1754 Evaluate side-chains 130 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 463 ASN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11360 Z= 0.215 Angle : 0.665 12.956 15446 Z= 0.345 Chirality : 0.044 0.204 1687 Planarity : 0.005 0.061 2036 Dihedral : 6.025 37.960 1563 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.71 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.81 (0.22), residues: 1416 helix: 0.30 (0.29), residues: 310 sheet: -1.89 (0.27), residues: 355 loop : -2.90 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 776 HIS 0.004 0.001 HIS D 139 PHE 0.047 0.002 PHE E 77 TYR 0.020 0.002 TYR D 79 ARG 0.008 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8703 (tmmt) cc_final: 0.8432 (tmtt) REVERT: A 368 GLU cc_start: 0.8195 (mm-30) cc_final: 0.6959 (tp30) REVERT: A 396 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 539 MET cc_start: 0.7208 (tpp) cc_final: 0.6979 (tpp) REVERT: A 711 MET cc_start: 0.8719 (ttt) cc_final: 0.8330 (ttm) REVERT: B 298 LEU cc_start: 0.8642 (pt) cc_final: 0.8411 (pt) REVERT: C 83 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8239 (mmm160) REVERT: D 34 GLU cc_start: 0.9615 (tp30) cc_final: 0.9346 (tp30) REVERT: D 169 PHE cc_start: 0.7983 (t80) cc_final: 0.7668 (t80) REVERT: E 46 ILE cc_start: 0.7557 (mm) cc_final: 0.7152 (mm) REVERT: E 71 ASN cc_start: 0.7104 (t0) cc_final: 0.6704 (t0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2145 time to fit residues: 49.2207 Evaluate side-chains 128 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 223 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11360 Z= 0.197 Angle : 0.670 12.251 15446 Z= 0.349 Chirality : 0.044 0.275 1687 Planarity : 0.005 0.064 2036 Dihedral : 5.939 37.905 1563 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.94 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.69 (0.22), residues: 1416 helix: 0.31 (0.29), residues: 309 sheet: -1.80 (0.27), residues: 357 loop : -2.79 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 776 HIS 0.005 0.001 HIS E 83 PHE 0.047 0.002 PHE D 64 TYR 0.031 0.002 TYR D 79 ARG 0.006 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8675 (tmmt) cc_final: 0.8384 (tmtt) REVERT: A 368 GLU cc_start: 0.8180 (mm-30) cc_final: 0.6935 (tp30) REVERT: A 472 SER cc_start: 0.8416 (t) cc_final: 0.8200 (p) REVERT: A 711 MET cc_start: 0.8685 (ttt) cc_final: 0.8303 (ttm) REVERT: B 298 LEU cc_start: 0.8569 (pt) cc_final: 0.8273 (pt) REVERT: D 34 GLU cc_start: 0.9631 (tp30) cc_final: 0.9385 (tp30) REVERT: D 111 MET cc_start: 0.9074 (mmt) cc_final: 0.8701 (mmp) REVERT: E 46 ILE cc_start: 0.7493 (mm) cc_final: 0.7068 (mm) REVERT: E 107 LYS cc_start: 0.8010 (tptp) cc_final: 0.7715 (tmtt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2245 time to fit residues: 51.3663 Evaluate side-chains 127 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 463 ASN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11360 Z= 0.178 Angle : 0.683 18.008 15446 Z= 0.347 Chirality : 0.044 0.178 1687 Planarity : 0.005 0.068 2036 Dihedral : 5.763 38.959 1563 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.44 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.53 (0.22), residues: 1416 helix: 0.51 (0.29), residues: 309 sheet: -1.68 (0.27), residues: 357 loop : -2.73 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 776 HIS 0.007 0.001 HIS D 139 PHE 0.031 0.002 PHE E 77 TYR 0.016 0.001 TYR D 79 ARG 0.006 0.001 ARG D 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8273 (tmtt) REVERT: A 368 GLU cc_start: 0.8159 (mm-30) cc_final: 0.6921 (tp30) REVERT: A 711 MET cc_start: 0.8662 (ttt) cc_final: 0.8288 (ttm) REVERT: B 298 LEU cc_start: 0.8496 (pt) cc_final: 0.8235 (pt) REVERT: D 34 GLU cc_start: 0.9628 (tp30) cc_final: 0.9337 (tp30) REVERT: D 169 PHE cc_start: 0.7864 (t80) cc_final: 0.7654 (t80) REVERT: E 46 ILE cc_start: 0.7376 (mm) cc_final: 0.6975 (mm) REVERT: E 107 LYS cc_start: 0.7865 (tptp) cc_final: 0.7625 (tmtt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2245 time to fit residues: 56.1981 Evaluate side-chains 134 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 0.0470 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.069255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.056072 restraints weight = 68774.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.057493 restraints weight = 45588.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.058494 restraints weight = 33854.520| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11360 Z= 0.194 Angle : 0.683 16.273 15446 Z= 0.350 Chirality : 0.044 0.174 1687 Planarity : 0.005 0.068 2036 Dihedral : 5.676 34.839 1563 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.37 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.52 (0.22), residues: 1416 helix: 0.38 (0.29), residues: 311 sheet: -1.61 (0.27), residues: 361 loop : -2.70 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 546 HIS 0.007 0.001 HIS D 139 PHE 0.033 0.002 PHE D 95 TYR 0.044 0.002 TYR D 79 ARG 0.005 0.000 ARG D 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.41 seconds wall clock time: 42 minutes 55.97 seconds (2575.97 seconds total)