Starting phenix.real_space_refine on Tue Jul 29 08:56:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyu_30018/07_2025/6lyu_30018.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyu_30018/07_2025/6lyu_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_30018/07_2025/6lyu_30018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyu_30018/07_2025/6lyu_30018.map" model { file = "/net/cci-nas-00/data/ceres_data/6lyu_30018/07_2025/6lyu_30018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyu_30018/07_2025/6lyu_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.97, per 1000 atoms: 0.63 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: 3.37 Conformation dependent library (CDL) restraints added in 1.4 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: 1.35 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: 3.70 Time building geometry restraints manager: 3.90 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: 1.380 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 29.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 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= 0.522 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 Details of bonding type rmsd hydrogen bonds : bond 0.27657 ( 377) hydrogen bonds : angle 10.61706 ( 1083) covalent geometry : bond 0.00918 (11360) covalent geometry : angle 1.16492 (15446) *********************** 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 : 1.277 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: 0.2468 time to fit residues: 58.2209 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 : 1.331 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.066535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053176 restraints weight = 67201.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054719 restraints weight = 42268.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055705 restraints weight = 30431.169| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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= 0.175 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 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 377) hydrogen bonds : angle 7.35277 ( 1083) covalent geometry : bond 0.00373 (11360) covalent geometry : angle 0.81730 (15446) *********************** 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 : 1.398 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 337 LEU cc_start: 0.8847 (tp) cc_final: 0.8483 (tp) REVERT: A 545 MET cc_start: 0.9170 (mtt) cc_final: 0.8812 (mtt) REVERT: A 686 TYR cc_start: 0.8526 (m-80) cc_final: 0.8303 (m-80) REVERT: B 127 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8904 (mt-10) REVERT: C 34 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7739 (tm-30) REVERT: E 71 ASN cc_start: 0.7825 (t0) cc_final: 0.6935 (t0) REVERT: E 95 PHE cc_start: 0.8941 (m-80) cc_final: 0.7709 (m-80) outliers start: 3 outliers final: 1 residues processed: 195 average time/residue: 0.2621 time to fit residues: 71.5689 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 : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 0.0000 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.065799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052335 restraints weight = 69021.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.053835 restraints weight = 44083.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054870 restraints weight = 32104.226| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11360 Z= 0.210 Angle : 0.777 11.509 15446 Z= 0.408 Chirality : 0.047 0.194 1687 Planarity : 0.005 0.066 2036 Dihedral : 7.026 39.320 1563 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.84 % Favored : 85.88 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: -4.06 (0.20), residues: 1416 helix: -0.82 (0.27), residues: 310 sheet: -2.72 (0.26), residues: 355 loop : -3.63 (0.20), residues: 751 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 0.055 0.002 PHE B 42 TYR 0.033 0.002 TYR A 618 ARG 0.008 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 377) hydrogen bonds : angle 6.93399 ( 1083) covalent geometry : bond 0.00447 (11360) covalent geometry : angle 0.77681 (15446) *********************** 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 : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8192 (mm-30) cc_final: 0.6970 (tp30) REVERT: A 396 GLU cc_start: 0.8726 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 534 ASN cc_start: 0.8537 (m-40) cc_final: 0.8282 (m-40) REVERT: A 539 MET cc_start: 0.7720 (mmm) cc_final: 0.7285 (tpp) REVERT: A 545 MET cc_start: 0.9113 (mtt) cc_final: 0.8682 (mtt) REVERT: A 686 TYR cc_start: 0.8450 (m-80) cc_final: 0.8243 (m-80) REVERT: A 711 MET cc_start: 0.8932 (ttt) cc_final: 0.8617 (ttm) REVERT: B 226 MET cc_start: 0.8598 (ttm) cc_final: 0.8385 (tpp) REVERT: D 58 LEU cc_start: 0.8755 (tp) cc_final: 0.8376 (tp) REVERT: E 71 ASN cc_start: 0.7955 (t0) cc_final: 0.7723 (t0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2600 time to fit residues: 62.8203 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 : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 64 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 324 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051731 restraints weight = 71312.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.053209 restraints weight = 45543.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054217 restraints weight = 33251.522| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11360 Z= 0.220 Angle : 0.759 11.594 15446 Z= 0.400 Chirality : 0.046 0.162 1687 Planarity : 0.006 0.104 2036 Dihedral : 6.898 42.577 1563 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.12 % Favored : 85.59 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -3.83 (0.21), residues: 1416 helix: -0.57 (0.28), residues: 315 sheet: -2.70 (0.26), residues: 370 loop : -3.45 (0.21), residues: 731 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 0.019 0.002 PHE A 738 TYR 0.028 0.002 TYR B 263 ARG 0.007 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 377) hydrogen bonds : angle 6.69053 ( 1083) covalent geometry : bond 0.00464 (11360) covalent geometry : angle 0.75940 (15446) *********************** 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 159 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.382 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: 0.7745 (mtmt) cc_final: 0.7430 (mppt) REVERT: A 368 GLU cc_start: 0.8231 (mm-30) cc_final: 0.6919 (tp30) REVERT: A 396 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 534 ASN cc_start: 0.8738 (m-40) cc_final: 0.8380 (m-40) REVERT: A 618 TYR cc_start: 0.8902 (m-10) cc_final: 0.8605 (m-10) REVERT: A 711 MET cc_start: 0.8805 (ttt) cc_final: 0.8544 (ttm) REVERT: D 79 TYR cc_start: 0.8661 (m-10) cc_final: 0.7805 (m-10) REVERT: D 169 PHE cc_start: 0.8333 (t80) cc_final: 0.8025 (t80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2333 time to fit residues: 54.0169 Evaluate side-chains 130 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 265 GLN A 748 ASN A 803 GLN B 121 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.065207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052207 restraints weight = 69586.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.053594 restraints weight = 46365.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054565 restraints weight = 34412.544| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11360 Z= 0.206 Angle : 0.747 11.162 15446 Z= 0.392 Chirality : 0.046 0.190 1687 Planarity : 0.005 0.051 2036 Dihedral : 6.784 42.801 1563 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.98 % Favored : 85.88 % 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 : 0.22 % 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: -3.66 (0.21), residues: 1416 helix: -0.52 (0.28), residues: 316 sheet: -2.52 (0.27), residues: 357 loop : -3.34 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 48 HIS 0.005 0.001 HIS D 139 PHE 0.039 0.002 PHE E 77 TYR 0.021 0.002 TYR C 65 ARG 0.010 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 377) hydrogen bonds : angle 6.63633 ( 1083) covalent geometry : bond 0.00439 (11360) covalent geometry : angle 0.74653 (15446) *********************** 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 164 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.423 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 307 ASP cc_start: 0.8818 (m-30) cc_final: 0.8399 (m-30) REVERT: A 368 GLU cc_start: 0.8212 (mm-30) cc_final: 0.6897 (tp30) REVERT: A 396 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 545 MET cc_start: 0.9307 (mtp) cc_final: 0.9092 (mtp) REVERT: A 618 TYR cc_start: 0.8969 (m-10) cc_final: 0.8680 (m-10) REVERT: A 648 PHE cc_start: 0.8171 (p90) cc_final: 0.7524 (p90) REVERT: A 711 MET cc_start: 0.8781 (ttt) cc_final: 0.8301 (ttm) REVERT: B 378 LEU cc_start: 0.9605 (tp) cc_final: 0.9338 (tt) REVERT: B 380 ILE cc_start: 0.9476 (mp) cc_final: 0.9268 (mp) REVERT: D 79 TYR cc_start: 0.8338 (m-10) cc_final: 0.7666 (m-80) REVERT: D 109 MET cc_start: 0.5750 (ppp) cc_final: 0.5466 (ppp) REVERT: D 169 PHE cc_start: 0.8364 (t80) cc_final: 0.7994 (t80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2928 time to fit residues: 70.9754 Evaluate side-chains 126 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN B 85 ASN B 165 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS D 44 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.068336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054996 restraints weight = 68680.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056500 restraints weight = 45733.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057520 restraints weight = 33778.049| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11360 Z= 0.143 Angle : 0.712 12.360 15446 Z= 0.371 Chirality : 0.046 0.201 1687 Planarity : 0.005 0.056 2036 Dihedral : 6.396 42.008 1563 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: -3.33 (0.22), residues: 1416 helix: -0.24 (0.28), residues: 313 sheet: -2.34 (0.27), residues: 361 loop : -3.11 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 776 HIS 0.004 0.001 HIS B 165 PHE 0.057 0.002 PHE D 128 TYR 0.016 0.002 TYR E 37 ARG 0.005 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 377) hydrogen bonds : angle 6.18113 ( 1083) covalent geometry : bond 0.00304 (11360) covalent geometry : angle 0.71228 (15446) *********************** 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 171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.421 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 304 MET cc_start: 0.8669 (ttm) cc_final: 0.8445 (ttm) REVERT: A 307 ASP cc_start: 0.8771 (m-30) cc_final: 0.8503 (m-30) REVERT: A 349 VAL cc_start: 0.9181 (t) cc_final: 0.8947 (p) REVERT: A 368 GLU cc_start: 0.8041 (mm-30) cc_final: 0.6720 (tp30) REVERT: A 396 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 618 TYR cc_start: 0.8951 (m-10) cc_final: 0.8699 (m-10) REVERT: A 711 MET cc_start: 0.8682 (ttt) cc_final: 0.8190 (ttm) REVERT: B 63 LEU cc_start: 0.9245 (tp) cc_final: 0.9000 (tp) REVERT: D 34 GLU cc_start: 0.9571 (tp30) cc_final: 0.9349 (tp30) REVERT: D 109 MET cc_start: 0.5919 (ppp) cc_final: 0.5678 (ppp) REVERT: D 169 PHE cc_start: 0.8176 (t80) cc_final: 0.7896 (t80) REVERT: D 186 THR cc_start: 0.9291 (m) cc_final: 0.9089 (m) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2076 time to fit residues: 52.7795 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 : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.065935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052471 restraints weight = 69682.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.053960 restraints weight = 45002.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054972 restraints weight = 32894.976| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11360 Z= 0.211 Angle : 0.741 12.557 15446 Z= 0.389 Chirality : 0.046 0.237 1687 Planarity : 0.005 0.056 2036 Dihedral : 6.520 41.636 1563 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.27 % Favored : 85.59 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -3.43 (0.21), residues: 1416 helix: -0.38 (0.28), residues: 315 sheet: -2.48 (0.26), residues: 368 loop : -3.11 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 749 HIS 0.004 0.001 HIS D 139 PHE 0.041 0.002 PHE D 128 TYR 0.024 0.002 TYR A 754 ARG 0.007 0.001 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 377) hydrogen bonds : angle 6.27942 ( 1083) covalent geometry : bond 0.00453 (11360) covalent geometry : angle 0.74087 (15446) *********************** 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 : 1.459 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 307 ASP cc_start: 0.8698 (m-30) cc_final: 0.8410 (m-30) REVERT: A 368 GLU cc_start: 0.8210 (mm-30) cc_final: 0.6897 (tp30) REVERT: A 396 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 618 TYR cc_start: 0.8841 (m-10) cc_final: 0.8641 (m-10) REVERT: A 711 MET cc_start: 0.8689 (ttt) cc_final: 0.8166 (ttm) REVERT: B 298 LEU cc_start: 0.8970 (pt) cc_final: 0.8755 (pt) REVERT: B 378 LEU cc_start: 0.9570 (tp) cc_final: 0.9299 (tt) REVERT: D 34 GLU cc_start: 0.9614 (tp30) cc_final: 0.9393 (tp30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2943 time to fit residues: 71.5367 Evaluate side-chains 128 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.9462 ------------------------------------------------------------------------------- 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 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053275 restraints weight = 68485.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054785 restraints weight = 44567.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055833 restraints weight = 32545.809| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11360 Z= 0.169 Angle : 0.716 12.030 15446 Z= 0.375 Chirality : 0.045 0.167 1687 Planarity : 0.005 0.057 2036 Dihedral : 6.414 41.354 1563 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -3.25 (0.21), residues: 1416 helix: -0.12 (0.28), residues: 307 sheet: -2.36 (0.27), residues: 363 loop : -3.02 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 749 HIS 0.004 0.001 HIS D 139 PHE 0.031 0.002 PHE D 128 TYR 0.023 0.002 TYR A 754 ARG 0.007 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 377) hydrogen bonds : angle 6.06366 ( 1083) covalent geometry : bond 0.00367 (11360) covalent geometry : angle 0.71646 (15446) *********************** 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 163 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.238 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 307 ASP cc_start: 0.8690 (m-30) cc_final: 0.8392 (m-30) REVERT: A 368 GLU cc_start: 0.8173 (mm-30) cc_final: 0.6811 (tp30) REVERT: A 396 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 618 TYR cc_start: 0.8829 (m-10) cc_final: 0.8613 (m-10) REVERT: A 711 MET cc_start: 0.8587 (ttt) cc_final: 0.8030 (ttm) REVERT: D 34 GLU cc_start: 0.9621 (tp30) cc_final: 0.9391 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2219 time to fit residues: 53.1138 Evaluate side-chains 130 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 678 GLN ** 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** E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.063655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050304 restraints weight = 72380.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051763 restraints weight = 46769.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052753 restraints weight = 34216.806| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11360 Z= 0.308 Angle : 0.857 13.206 15446 Z= 0.445 Chirality : 0.049 0.178 1687 Planarity : 0.006 0.078 2036 Dihedral : 6.914 42.355 1563 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.11 % Favored : 84.82 % 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 : 0.29 % 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: -3.49 (0.21), residues: 1416 helix: -0.47 (0.27), residues: 308 sheet: -2.44 (0.26), residues: 363 loop : -3.15 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 776 HIS 0.005 0.001 HIS D 139 PHE 0.027 0.003 PHE A 395 TYR 0.032 0.003 TYR A 754 ARG 0.010 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 377) hydrogen bonds : angle 6.54884 ( 1083) covalent geometry : bond 0.00645 (11360) covalent geometry : angle 0.85685 (15446) *********************** 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 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.362 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 177 ILE cc_start: 0.8707 (mt) cc_final: 0.8485 (mt) REVERT: A 307 ASP cc_start: 0.8731 (m-30) cc_final: 0.8442 (m-30) REVERT: A 396 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 618 TYR cc_start: 0.8953 (m-10) cc_final: 0.8684 (m-10) REVERT: B 298 LEU cc_start: 0.8945 (pt) cc_final: 0.8684 (pt) REVERT: B 380 ILE cc_start: 0.9521 (mp) cc_final: 0.9316 (mp) REVERT: D 34 GLU cc_start: 0.9654 (tp30) cc_final: 0.9439 (tp30) REVERT: D 191 TRP cc_start: 0.8860 (m100) cc_final: 0.8519 (m100) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3039 time to fit residues: 66.9982 Evaluate side-chains 122 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 3 optimal weight: 0.0050 chunk 137 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN A 561 GLN ** 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 ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.067694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054103 restraints weight = 67872.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055631 restraints weight = 43811.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056670 restraints weight = 32002.719| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11360 Z= 0.145 Angle : 0.726 12.127 15446 Z= 0.376 Chirality : 0.046 0.168 1687 Planarity : 0.005 0.066 2036 Dihedral : 6.370 41.812 1563 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.95 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -3.12 (0.22), residues: 1416 helix: -0.05 (0.28), residues: 308 sheet: -2.29 (0.26), residues: 360 loop : -2.91 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 749 HIS 0.005 0.001 HIS D 139 PHE 0.024 0.002 PHE D 128 TYR 0.029 0.002 TYR D 79 ARG 0.008 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 377) hydrogen bonds : angle 5.93262 ( 1083) covalent geometry : bond 0.00323 (11360) covalent geometry : angle 0.72637 (15446) ********************** 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 165 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.427 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 307 ASP cc_start: 0.8619 (m-30) cc_final: 0.8311 (m-30) REVERT: A 368 GLU cc_start: 0.8119 (mm-30) cc_final: 0.6724 (tp30) REVERT: A 396 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 618 TYR cc_start: 0.8915 (m-10) cc_final: 0.8676 (m-10) REVERT: A 711 MET cc_start: 0.8792 (ttt) cc_final: 0.8403 (ttm) REVERT: B 298 LEU cc_start: 0.8886 (pt) cc_final: 0.8677 (pt) REVERT: D 34 GLU cc_start: 0.9657 (tp30) cc_final: 0.9443 (tp30) REVERT: D 169 PHE cc_start: 0.8264 (t80) cc_final: 0.8046 (t80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2533 time to fit residues: 62.8550 Evaluate side-chains 122 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 9.9990 chunk 109 optimal weight: 0.0060 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- 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 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 241 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 = 0.3591 r_free = 0.3591 target = 0.066831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053322 restraints weight = 69003.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054893 restraints weight = 44515.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055972 restraints weight = 32300.136| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5326 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= 0.172 Angle : 0.742 12.052 15446 Z= 0.384 Chirality : 0.046 0.173 1687 Planarity : 0.005 0.065 2036 Dihedral : 6.351 41.742 1563 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % 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: -3.16 (0.22), residues: 1416 helix: -0.19 (0.28), residues: 316 sheet: -2.27 (0.26), residues: 368 loop : -2.94 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 749 HIS 0.007 0.001 HIS D 139 PHE 0.039 0.002 PHE D 64 TYR 0.023 0.002 TYR A 754 ARG 0.006 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 377) hydrogen bonds : angle 5.90813 ( 1083) covalent geometry : bond 0.00374 (11360) covalent geometry : angle 0.74183 (15446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4383.46 seconds wall clock time: 80 minutes 38.60 seconds (4838.60 seconds total)