Starting phenix.real_space_refine on Sun Dec 29 19:05:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyu_30018/12_2024/6lyu_30018.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyu_30018/12_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/cci-nas-00/data/ceres_data/6lyu_30018/12_2024/6lyu_30018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyu_30018/12_2024/6lyu_30018.map" model { file = "/net/cci-nas-00/data/ceres_data/6lyu_30018/12_2024/6lyu_30018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyu_30018/12_2024/6lyu_30018.cif" } 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. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.83, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.6 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: 1.49 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: 3.83 Time building geometry restraints manager: 3.32 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: 0.00 - 4.95: 15359 4.95 - 9.91: 77 9.91 - 14.86: 4 14.86 - 19.81: 2 19.81 - 24.77: 4 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 3.040 nonbonded pdb=" OH TYR D 184 " pdb=" NH2 ARG D 188 " model vdw 1.989 3.120 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 3.120 nonbonded pdb=" O THR A 720 " pdb=" OG1 THR A 735 " model vdw 2.054 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.060 Find NCS groups from input model: 0.110 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 14 poor density : 156 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: 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: 0.2575 time to fit residues: 60.4078 Evaluate side-chains 122 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 185 ASN A 196 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 266 ASN B 287 ASN ** B 301 GLN ** 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 D 230 GLN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11360 Z= 0.245 Angle : 0.817 13.386 15446 Z= 0.433 Chirality : 0.049 0.161 1687 Planarity : 0.006 0.083 2036 Dihedral : 7.326 43.783 1563 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.70 % Favored : 85.95 % Rotamer: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.72 % 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: -4.65 (0.19), residues: 1416 helix: -1.52 (0.25), residues: 306 sheet: -3.09 (0.25), residues: 357 loop : -3.88 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 576 HIS 0.006 0.001 HIS B 165 PHE 0.023 0.002 PHE A 738 TYR 0.020 0.002 TYR D 62 ARG 0.006 0.001 ARG A 346 *********************** 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 196 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 1.082 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: A 303 LYS cc_start: 0.8941 (tttm) cc_final: 0.8728 (tmtt) REVERT: A 337 LEU cc_start: 0.8542 (tp) cc_final: 0.8168 (tp) REVERT: A 545 MET cc_start: 0.9067 (mtt) cc_final: 0.8732 (mtt) REVERT: A 686 TYR cc_start: 0.8559 (m-80) cc_final: 0.8332 (m-80) REVERT: E 71 ASN cc_start: 0.7560 (t0) cc_final: 0.7030 (t0) REVERT: E 95 PHE cc_start: 0.8437 (m-80) cc_final: 0.7508 (m-80) outliers start: 3 outliers final: 1 residues processed: 195 average time/residue: 0.2501 time to fit residues: 68.0107 Evaluate side-chains 139 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 561 GLN A 573 ASN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 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 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 241 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3597 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= 0.260 Angle : 0.761 11.192 15446 Z= 0.399 Chirality : 0.047 0.190 1687 Planarity : 0.005 0.060 2036 Dihedral : 6.921 39.313 1563 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.42 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -3.96 (0.20), residues: 1416 helix: -0.74 (0.27), residues: 310 sheet: -2.63 (0.26), residues: 351 loop : -3.58 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS E 83 PHE 0.045 0.002 PHE B 42 TYR 0.033 0.002 TYR A 618 ARG 0.015 0.001 ARG B 392 *********************** 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 173 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.285 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: A 303 LYS cc_start: 0.8720 (tttm) cc_final: 0.8516 (tmtt) REVERT: A 368 GLU cc_start: 0.8081 (mm-30) cc_final: 0.6948 (tp30) REVERT: A 396 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 534 ASN cc_start: 0.8465 (m-40) cc_final: 0.8209 (m-40) REVERT: A 545 MET cc_start: 0.9027 (mtt) cc_final: 0.8786 (mtt) REVERT: A 686 TYR cc_start: 0.8518 (m-80) cc_final: 0.8314 (m-80) REVERT: A 711 MET cc_start: 0.8825 (ttt) cc_final: 0.8549 (ttm) REVERT: B 391 THR cc_start: 0.7565 (t) cc_final: 0.7334 (m) REVERT: D 58 LEU cc_start: 0.8765 (tp) cc_final: 0.8372 (tp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2744 time to fit residues: 66.0304 Evaluate side-chains 133 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 88 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: 0.8078 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11360 Z= 0.373 Angle : 0.801 12.295 15446 Z= 0.421 Chirality : 0.047 0.174 1687 Planarity : 0.006 0.076 2036 Dihedral : 7.036 42.910 1563 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.62 % Favored : 85.17 % 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 : 0.00 % 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: -3.92 (0.21), residues: 1416 helix: -0.71 (0.27), residues: 314 sheet: -2.73 (0.26), residues: 374 loop : -3.48 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 546 HIS 0.005 0.001 HIS D 139 PHE 0.025 0.003 PHE E 77 TYR 0.024 0.002 TYR C 65 ARG 0.010 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 155 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.326 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: A 251 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7641 (mppt) REVERT: A 303 LYS cc_start: 0.8822 (tttm) cc_final: 0.8577 (tmtt) REVERT: A 380 ASP cc_start: 0.8609 (p0) cc_final: 0.8405 (p0) REVERT: A 396 GLU cc_start: 0.8706 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 534 ASN cc_start: 0.8636 (m-40) cc_final: 0.8255 (m-40) REVERT: A 618 TYR cc_start: 0.8887 (m-10) cc_final: 0.8616 (m-10) REVERT: A 711 MET cc_start: 0.8761 (ttt) cc_final: 0.8335 (ttm) REVERT: B 378 LEU cc_start: 0.9392 (tp) cc_final: 0.9094 (tt) REVERT: D 79 TYR cc_start: 0.8695 (m-10) cc_final: 0.7884 (m-10) REVERT: D 109 MET cc_start: 0.7049 (tmm) cc_final: 0.6786 (ppp) REVERT: D 117 MET cc_start: 0.8915 (tpp) cc_final: 0.8606 (tpp) REVERT: D 169 PHE cc_start: 0.8141 (t80) cc_final: 0.7857 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2320 time to fit residues: 52.5010 Evaluate side-chains 124 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN B 121 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS E 33 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 79 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11360 Z= 0.477 Angle : 0.896 12.887 15446 Z= 0.471 Chirality : 0.050 0.198 1687 Planarity : 0.006 0.050 2036 Dihedral : 7.498 42.641 1563 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 33.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.10 % Favored : 83.76 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -4.10 (0.21), residues: 1416 helix: -0.98 (0.26), residues: 310 sheet: -2.84 (0.26), residues: 375 loop : -3.52 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 776 HIS 0.006 0.002 HIS D 139 PHE 0.037 0.003 PHE E 77 TYR 0.033 0.003 TYR C 65 ARG 0.011 0.001 ARG E 47 *********************** 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 139 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 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: 0.8897 (tttm) cc_final: 0.8675 (tmtt) REVERT: A 396 GLU cc_start: 0.8777 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 618 TYR cc_start: 0.9002 (m-10) cc_final: 0.8671 (m-10) REVERT: A 711 MET cc_start: 0.8670 (ttt) cc_final: 0.8119 (ttm) REVERT: B 226 MET cc_start: 0.8172 (tpp) cc_final: 0.7776 (tmm) REVERT: C 83 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8599 (mmt90) REVERT: D 79 TYR cc_start: 0.8524 (m-10) cc_final: 0.7785 (m-80) REVERT: E 38 LEU cc_start: 0.8163 (pp) cc_final: 0.7898 (pp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2231 time to fit residues: 45.3851 Evaluate side-chains 116 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 748 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 44 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11360 Z= 0.252 Angle : 0.745 11.005 15446 Z= 0.391 Chirality : 0.046 0.206 1687 Planarity : 0.005 0.052 2036 Dihedral : 6.862 42.187 1563 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.06 % Favored : 86.79 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.69 (0.21), residues: 1416 helix: -0.62 (0.28), residues: 313 sheet: -2.59 (0.26), residues: 357 loop : -3.27 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 776 HIS 0.005 0.001 HIS B 165 PHE 0.026 0.002 PHE A 395 TYR 0.022 0.002 TYR E 37 ARG 0.007 0.001 ARG A 346 *********************** 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 161 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.192 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: 0.8757 (tttm) cc_final: 0.8530 (tmtt) REVERT: A 396 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 618 TYR cc_start: 0.8893 (m-10) cc_final: 0.8615 (m-10) REVERT: A 711 MET cc_start: 0.8570 (ttt) cc_final: 0.8076 (ttm) REVERT: A 774 LEU cc_start: 0.8811 (mt) cc_final: 0.8453 (mt) REVERT: B 226 MET cc_start: 0.8204 (tpp) cc_final: 0.7753 (tmm) REVERT: C 56 MET cc_start: 0.6734 (mtm) cc_final: 0.5718 (mtt) REVERT: C 83 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8426 (mmt90) REVERT: D 34 GLU cc_start: 0.9577 (tp30) cc_final: 0.9307 (tp30) REVERT: D 117 MET cc_start: 0.8817 (tpp) cc_final: 0.8521 (tpp) REVERT: D 169 PHE cc_start: 0.7988 (t80) cc_final: 0.7677 (t80) REVERT: E 71 ASN cc_start: 0.7741 (t0) cc_final: 0.7185 (t0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2276 time to fit residues: 53.5506 Evaluate side-chains 121 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** 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 324 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4679 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= 0.231 Angle : 0.728 13.136 15446 Z= 0.379 Chirality : 0.046 0.166 1687 Planarity : 0.005 0.055 2036 Dihedral : 6.571 41.685 1563 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.05 % Favored : 85.81 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.48 (0.21), residues: 1416 helix: -0.47 (0.28), residues: 314 sheet: -2.53 (0.26), residues: 360 loop : -3.09 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 776 HIS 0.004 0.001 HIS E 83 PHE 0.021 0.002 PHE E 77 TYR 0.025 0.002 TYR E 37 ARG 0.007 0.001 ARG B 295 *********************** 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 161 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.266 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: 0.8722 (tttm) cc_final: 0.8521 (tmtt) REVERT: A 368 GLU cc_start: 0.8104 (mm-30) cc_final: 0.6826 (tp30) REVERT: A 396 GLU cc_start: 0.8721 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 618 TYR cc_start: 0.8941 (m-10) cc_final: 0.8679 (m-10) REVERT: A 711 MET cc_start: 0.8573 (ttt) cc_final: 0.8071 (ttm) REVERT: B 226 MET cc_start: 0.8173 (tpp) cc_final: 0.7720 (tmm) REVERT: B 298 LEU cc_start: 0.8683 (pt) cc_final: 0.8463 (pt) REVERT: C 83 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8358 (mmt90) REVERT: D 34 GLU cc_start: 0.9609 (tp30) cc_final: 0.9345 (tp30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2372 time to fit residues: 54.9545 Evaluate side-chains 124 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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: 6.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 165 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11360 Z= 0.208 Angle : 0.724 12.428 15446 Z= 0.373 Chirality : 0.045 0.149 1687 Planarity : 0.005 0.059 2036 Dihedral : 6.402 41.605 1563 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.78 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % 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: -3.28 (0.22), residues: 1416 helix: -0.34 (0.28), residues: 314 sheet: -2.33 (0.27), residues: 356 loop : -2.99 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 749 HIS 0.004 0.001 HIS D 139 PHE 0.024 0.002 PHE E 77 TYR 0.026 0.002 TYR E 37 ARG 0.017 0.001 ARG B 195 *********************** 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 164 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.295 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: 0.8743 (tttm) cc_final: 0.8532 (tmtt) REVERT: A 368 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7013 (tp30) REVERT: A 396 GLU cc_start: 0.8761 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 618 TYR cc_start: 0.8938 (m-10) cc_final: 0.8695 (m-10) REVERT: A 648 PHE cc_start: 0.7625 (p90) cc_final: 0.7220 (p90) REVERT: A 711 MET cc_start: 0.8504 (ttt) cc_final: 0.8006 (ttm) REVERT: B 226 MET cc_start: 0.8199 (tpp) cc_final: 0.7766 (tmm) REVERT: C 83 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8465 (mmt90) REVERT: D 34 GLU cc_start: 0.9616 (tp30) cc_final: 0.9376 (tp30) REVERT: D 109 MET cc_start: 0.5849 (ppp) cc_final: 0.5523 (ppp) REVERT: E 107 LYS cc_start: 0.8219 (tptp) cc_final: 0.7880 (tptp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2421 time to fit residues: 56.9402 Evaluate side-chains 129 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 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 542 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5307 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= 0.205 Angle : 0.715 13.210 15446 Z= 0.367 Chirality : 0.045 0.170 1687 Planarity : 0.005 0.064 2036 Dihedral : 6.233 41.987 1563 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -3.18 (0.21), residues: 1416 helix: -0.41 (0.27), residues: 313 sheet: -2.11 (0.27), residues: 344 loop : -2.95 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 191 HIS 0.004 0.001 HIS D 139 PHE 0.018 0.002 PHE A 347 TYR 0.033 0.002 TYR D 79 ARG 0.009 0.001 ARG D 197 *********************** 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 168 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.171 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: 0.8677 (tttm) cc_final: 0.8471 (tmtt) REVERT: A 368 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7008 (tp30) REVERT: A 396 GLU cc_start: 0.8797 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 618 TYR cc_start: 0.8920 (m-10) cc_final: 0.8681 (m-10) REVERT: B 226 MET cc_start: 0.8172 (tpp) cc_final: 0.7774 (tmm) REVERT: B 378 LEU cc_start: 0.9262 (tp) cc_final: 0.8992 (tt) REVERT: B 381 GLN cc_start: 0.8365 (tt0) cc_final: 0.8073 (tm-30) REVERT: C 83 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8489 (mmt90) REVERT: D 34 GLU cc_start: 0.9644 (tp30) cc_final: 0.9409 (tp30) REVERT: D 109 MET cc_start: 0.5874 (ppp) cc_final: 0.5665 (ppp) REVERT: D 169 PHE cc_start: 0.7983 (t80) cc_final: 0.7758 (t80) REVERT: E 71 ASN cc_start: 0.7357 (t0) cc_final: 0.7042 (t0) REVERT: E 107 LYS cc_start: 0.8237 (tptp) cc_final: 0.7810 (tmtt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2478 time to fit residues: 59.7023 Evaluate side-chains 129 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5635 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= 0.200 Angle : 0.731 12.721 15446 Z= 0.377 Chirality : 0.046 0.171 1687 Planarity : 0.005 0.067 2036 Dihedral : 6.111 41.596 1563 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % 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: -3.05 (0.21), residues: 1416 helix: -0.37 (0.27), residues: 314 sheet: -1.94 (0.27), residues: 344 loop : -2.88 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 776 HIS 0.006 0.001 HIS D 139 PHE 0.054 0.002 PHE D 64 TYR 0.035 0.002 TYR B 263 ARG 0.006 0.001 ARG A 583 ********************** 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 171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.186 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: 0.8625 (tttm) cc_final: 0.8289 (tmtt) REVERT: A 368 GLU cc_start: 0.7935 (mm-30) cc_final: 0.6896 (tp30) REVERT: A 396 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 618 TYR cc_start: 0.8898 (m-10) cc_final: 0.8661 (m-10) REVERT: A 711 MET cc_start: 0.8679 (ttt) cc_final: 0.8396 (ttm) REVERT: A 774 LEU cc_start: 0.8527 (mt) cc_final: 0.8310 (mp) REVERT: B 51 SER cc_start: 0.8997 (m) cc_final: 0.8544 (t) REVERT: B 226 MET cc_start: 0.8163 (tpp) cc_final: 0.7732 (tmm) REVERT: B 378 LEU cc_start: 0.9247 (tp) cc_final: 0.9008 (tt) REVERT: C 83 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8479 (mmt90) REVERT: D 34 GLU cc_start: 0.9649 (tp30) cc_final: 0.9405 (tp30) REVERT: D 145 SER cc_start: 0.9191 (m) cc_final: 0.8917 (p) REVERT: D 169 PHE cc_start: 0.8043 (t80) cc_final: 0.7825 (t80) REVERT: D 199 GLU cc_start: 0.8512 (mp0) cc_final: 0.8245 (mp0) REVERT: E 107 LYS cc_start: 0.8074 (tptp) cc_final: 0.7855 (tmtt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2579 time to fit residues: 63.0441 Evaluate side-chains 131 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 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** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.066316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053112 restraints weight = 69666.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054493 restraints weight = 46265.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055447 restraints weight = 34472.338| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11360 Z= 0.293 Angle : 0.760 13.751 15446 Z= 0.395 Chirality : 0.046 0.167 1687 Planarity : 0.005 0.063 2036 Dihedral : 6.367 41.228 1563 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % 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: -3.20 (0.21), residues: 1416 helix: -0.51 (0.27), residues: 316 sheet: -2.13 (0.26), residues: 369 loop : -2.92 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 749 HIS 0.008 0.001 HIS D 139 PHE 0.033 0.002 PHE D 95 TYR 0.031 0.002 TYR D 79 ARG 0.005 0.001 ARG A 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.25 seconds wall clock time: 44 minutes 44.43 seconds (2684.43 seconds total)