Starting phenix.real_space_refine on Wed Mar 4 05:31:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyu_30018/03_2026/6lyu_30018.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyu_30018/03_2026/6lyu_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 { model { file = "/net/cci-nas-00/data/ceres_data/6lyu_30018/03_2026/6lyu_30018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyu_30018/03_2026/6lyu_30018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lyu_30018/03_2026/6lyu_30018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyu_30018/03_2026/6lyu_30018.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 2} 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: 2.31, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 593.4 milliseconds 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: 0.28 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: 1.90 Time building geometry restraints manager: 1.26 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: 1.640 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- 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 : 57.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.016 0.001 ARG D 212 TYR 0.035 0.003 TYR B 73 PHE 0.028 0.003 PHE A 791 TRP 0.031 0.003 TRP A 749 HIS 0.011 0.002 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00918 (11360) covalent geometry : angle 1.16492 (15446) hydrogen bonds : bond 0.27657 ( 377) hydrogen bonds : angle 10.61706 ( 1083) *********************** 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 : 0.455 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: 0.8445 (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: 0.6190 (p) REVERT: A 552 MET cc_start: 0.8979 (mmm) cc_final: 0.8757 (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: 0.8381 (mm-30) REVERT: D 34 GLU cc_start: 0.9662 (tp30) cc_final: 0.9353 (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: 0.8618 (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: 0.8361 (pm20) outliers start: 14 outliers final: 3 residues processed: 167 average time/residue: 0.1073 time to fit residues: 25.5445 Evaluate side-chains 121 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 561 GLN A 573 ASN ** 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 172 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.065823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052521 restraints weight = 68006.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.054070 restraints weight = 42661.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055102 restraints weight = 30620.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055832 restraints weight = 24159.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056296 restraints weight = 20370.520| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11360 Z= 0.185 Angle : 0.823 13.419 15446 Z= 0.436 Chirality : 0.049 0.174 1687 Planarity : 0.006 0.094 2036 Dihedral : 7.415 43.560 1563 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.05 % Favored : 85.59 % Rotamer: Outliers : 0.25 % Allowed : 8.61 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.19), residues: 1416 helix: -1.67 (0.25), residues: 307 sheet: -3.06 (0.25), residues: 351 loop : -3.96 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 97 TYR 0.022 0.002 TYR B 263 PHE 0.023 0.002 PHE A 738 TRP 0.022 0.002 TRP A 749 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00393 (11360) covalent geometry : angle 0.82268 (15446) hydrogen bonds : bond 0.05058 ( 377) hydrogen bonds : angle 7.43506 ( 1083) *********************** 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 188 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.409 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 251 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7501 (mppt) REVERT: A 337 LEU cc_start: 0.8832 (tp) cc_final: 0.8479 (tp) REVERT: A 545 MET cc_start: 0.9178 (mtt) cc_final: 0.8935 (mtt) REVERT: A 686 TYR cc_start: 0.8440 (m-80) cc_final: 0.8220 (m-80) REVERT: E 71 ASN cc_start: 0.7820 (t0) cc_final: 0.6995 (t0) REVERT: E 95 PHE cc_start: 0.8867 (m-80) cc_final: 0.7613 (m-80) outliers start: 3 outliers final: 1 residues processed: 187 average time/residue: 0.1063 time to fit residues: 27.8680 Evaluate side-chains 132 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.0050 chunk 114 optimal weight: 4.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 538 ASN ** A 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 D 44 GLN ** 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 = 0.3565 r_free = 0.3565 target = 0.065702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052605 restraints weight = 70109.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054048 restraints weight = 45871.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054951 restraints weight = 33742.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055670 restraints weight = 27216.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.056097 restraints weight = 23213.825| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11360 Z= 0.210 Angle : 0.786 11.717 15446 Z= 0.413 Chirality : 0.048 0.184 1687 Planarity : 0.006 0.077 2036 Dihedral : 7.096 39.465 1563 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.98 % Favored : 85.73 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.20), residues: 1416 helix: -0.93 (0.27), residues: 311 sheet: -2.82 (0.26), residues: 360 loop : -3.63 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 366 TYR 0.031 0.002 TYR A 618 PHE 0.047 0.002 PHE B 42 TRP 0.027 0.002 TRP D 48 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00449 (11360) covalent geometry : angle 0.78643 (15446) hydrogen bonds : bond 0.04673 ( 377) hydrogen bonds : angle 7.00270 ( 1083) *********************** 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 167 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.387 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 303 LYS cc_start: 0.8820 (tmmt) cc_final: 0.8606 (tmtt) REVERT: A 368 GLU cc_start: 0.8172 (mm-30) cc_final: 0.6889 (tp30) REVERT: A 396 GLU cc_start: 0.8781 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 534 ASN cc_start: 0.8610 (m-40) cc_final: 0.8304 (m-40) REVERT: A 686 TYR cc_start: 0.8417 (m-80) cc_final: 0.8212 (m-80) REVERT: B 226 MET cc_start: 0.8653 (ttm) cc_final: 0.8335 (tpp) REVERT: D 58 LEU cc_start: 0.8763 (tp) cc_final: 0.8391 (tp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0948 time to fit residues: 22.9172 Evaluate side-chains 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 561 GLN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 803 GLN B 85 ASN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.068274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.054956 restraints weight = 68514.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.056433 restraints weight = 45137.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057461 restraints weight = 33318.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.058161 restraints weight = 26609.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.058650 restraints weight = 22633.934| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11360 Z= 0.141 Angle : 0.707 10.487 15446 Z= 0.370 Chirality : 0.046 0.160 1687 Planarity : 0.005 0.059 2036 Dihedral : 6.538 42.966 1563 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.08 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.64 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.21), residues: 1416 helix: -0.32 (0.29), residues: 309 sheet: -2.58 (0.25), residues: 377 loop : -3.27 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 734 TYR 0.025 0.002 TYR B 263 PHE 0.019 0.002 PHE D 128 TRP 0.019 0.002 TRP B 103 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00312 (11360) covalent geometry : angle 0.70712 (15446) hydrogen bonds : bond 0.03949 ( 377) hydrogen bonds : angle 6.36818 ( 1083) *********************** 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 181 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.353 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 303 LYS cc_start: 0.8699 (tmmt) cc_final: 0.8463 (tmtt) REVERT: A 349 VAL cc_start: 0.9123 (t) cc_final: 0.8900 (p) REVERT: A 368 GLU cc_start: 0.8028 (mm-30) cc_final: 0.6604 (tp30) REVERT: B 298 LEU cc_start: 0.8889 (pt) cc_final: 0.8683 (pt) REVERT: D 169 PHE cc_start: 0.8440 (t80) cc_final: 0.8163 (t80) REVERT: E 31 ASP cc_start: 0.8157 (m-30) cc_final: 0.7873 (t0) REVERT: E 38 LEU cc_start: 0.8179 (pp) cc_final: 0.7927 (pp) REVERT: E 46 ILE cc_start: 0.7841 (mm) cc_final: 0.7306 (mm) REVERT: E 50 MET cc_start: 0.7928 (ptp) cc_final: 0.7462 (ptp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0969 time to fit residues: 25.4331 Evaluate side-chains 140 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 83 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN B 121 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.066734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053463 restraints weight = 70406.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054900 restraints weight = 46826.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055880 restraints weight = 34755.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.056556 restraints weight = 27941.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.057033 restraints weight = 23831.427| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11360 Z= 0.188 Angle : 0.730 12.482 15446 Z= 0.383 Chirality : 0.045 0.154 1687 Planarity : 0.005 0.051 2036 Dihedral : 6.582 42.575 1563 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.57 % Favored : 87.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.21), residues: 1416 helix: -0.39 (0.28), residues: 315 sheet: -2.43 (0.26), residues: 357 loop : -3.24 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 33 TYR 0.022 0.002 TYR A 618 PHE 0.052 0.002 PHE D 128 TRP 0.023 0.002 TRP A 546 HIS 0.005 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00403 (11360) covalent geometry : angle 0.73013 (15446) hydrogen bonds : bond 0.04164 ( 377) hydrogen bonds : angle 6.43565 ( 1083) *********************** 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 : 0.294 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: 0.8745 (tmmt) cc_final: 0.8498 (tmtt) REVERT: A 368 GLU cc_start: 0.8178 (mm-30) cc_final: 0.6904 (tp30) REVERT: A 396 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 618 TYR cc_start: 0.8836 (m-10) cc_final: 0.8540 (m-10) REVERT: A 653 TYR cc_start: 0.7938 (m-80) cc_final: 0.7709 (m-80) REVERT: A 711 MET cc_start: 0.8722 (ttt) cc_final: 0.7736 (tmm) REVERT: B 63 LEU cc_start: 0.9254 (tp) cc_final: 0.9045 (tp) REVERT: B 298 LEU cc_start: 0.8896 (pt) cc_final: 0.8687 (pt) REVERT: B 378 LEU cc_start: 0.9575 (tp) cc_final: 0.9302 (tt) REVERT: D 34 GLU cc_start: 0.9553 (tp30) cc_final: 0.9268 (tp30) REVERT: D 169 PHE cc_start: 0.8425 (t80) cc_final: 0.8136 (t80) REVERT: E 71 ASN cc_start: 0.7710 (t0) cc_final: 0.6955 (t0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0911 time to fit residues: 21.7541 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.064893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051591 restraints weight = 70130.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053069 restraints weight = 45084.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054053 restraints weight = 32851.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054725 restraints weight = 26127.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055250 restraints weight = 22222.050| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11360 Z= 0.251 Angle : 0.786 12.850 15446 Z= 0.412 Chirality : 0.047 0.211 1687 Planarity : 0.005 0.060 2036 Dihedral : 6.823 41.979 1563 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.84 % Favored : 86.02 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.21), residues: 1416 helix: -0.50 (0.28), residues: 317 sheet: -2.61 (0.26), residues: 375 loop : -3.18 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 212 TYR 0.026 0.002 TYR E 37 PHE 0.039 0.002 PHE D 128 TRP 0.023 0.002 TRP A 546 HIS 0.005 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00527 (11360) covalent geometry : angle 0.78609 (15446) hydrogen bonds : bond 0.04489 ( 377) hydrogen bonds : angle 6.58024 ( 1083) *********************** 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 148 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.404 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: 0.8774 (tmmt) cc_final: 0.8544 (tmtt) REVERT: A 396 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 298 LEU cc_start: 0.8954 (pt) cc_final: 0.8689 (pt) REVERT: B 378 LEU cc_start: 0.9585 (tp) cc_final: 0.9308 (tt) REVERT: C 83 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8475 (mmt90) REVERT: D 34 GLU cc_start: 0.9601 (tp30) cc_final: 0.9315 (tp30) REVERT: D 109 MET cc_start: 0.5772 (ppp) cc_final: 0.5455 (ppp) REVERT: D 145 SER cc_start: 0.9062 (m) cc_final: 0.8778 (p) REVERT: D 178 GLU cc_start: 0.8654 (mp0) cc_final: 0.8430 (mp0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0942 time to fit residues: 20.4134 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 : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 678 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 347 HIS D 44 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049947 restraints weight = 71347.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051381 restraints weight = 45672.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052386 restraints weight = 33148.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053071 restraints weight = 26383.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053551 restraints weight = 22361.970| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 11360 Z= 0.315 Angle : 0.861 12.312 15446 Z= 0.453 Chirality : 0.049 0.189 1687 Planarity : 0.006 0.054 2036 Dihedral : 7.254 41.600 1563 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 30.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.11 % Favored : 84.75 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.21), residues: 1416 helix: -0.83 (0.27), residues: 311 sheet: -2.66 (0.26), residues: 372 loop : -3.30 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 295 TYR 0.032 0.003 TYR E 37 PHE 0.028 0.003 PHE D 128 TRP 0.053 0.003 TRP A 776 HIS 0.005 0.002 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00658 (11360) covalent geometry : angle 0.86075 (15446) hydrogen bonds : bond 0.04885 ( 377) hydrogen bonds : angle 6.97008 ( 1083) *********************** 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 146 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.468 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 177 ILE cc_start: 0.8930 (mt) cc_final: 0.8669 (mt) REVERT: A 303 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8519 (tmtt) REVERT: A 307 ASP cc_start: 0.8734 (m-30) cc_final: 0.8396 (m-30) REVERT: A 396 GLU cc_start: 0.8874 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 539 MET cc_start: 0.7493 (tpp) cc_final: 0.7261 (tpp) REVERT: A 711 MET cc_start: 0.8779 (ttt) cc_final: 0.8562 (ttt) REVERT: A 774 LEU cc_start: 0.8814 (mt) cc_final: 0.8342 (mt) REVERT: B 380 ILE cc_start: 0.9519 (mp) cc_final: 0.9309 (mp) REVERT: C 83 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8742 (mmt90) REVERT: D 34 GLU cc_start: 0.9606 (tp30) cc_final: 0.9322 (tp30) REVERT: D 109 MET cc_start: 0.5792 (ppp) cc_final: 0.5485 (ppp) REVERT: D 145 SER cc_start: 0.9087 (m) cc_final: 0.8810 (p) REVERT: D 169 PHE cc_start: 0.8188 (t80) cc_final: 0.7850 (t80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1007 time to fit residues: 21.1995 Evaluate side-chains 117 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** 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 229 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.067881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054565 restraints weight = 67055.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056082 restraints weight = 43578.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057146 restraints weight = 31643.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057889 restraints weight = 25142.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058406 restraints weight = 21185.960| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11360 Z= 0.143 Angle : 0.733 11.637 15446 Z= 0.382 Chirality : 0.046 0.157 1687 Planarity : 0.005 0.061 2036 Dihedral : 6.567 41.813 1563 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.65 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.22), residues: 1416 helix: -0.41 (0.28), residues: 313 sheet: -2.35 (0.27), residues: 355 loop : -2.99 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 78 TYR 0.025 0.002 TYR E 37 PHE 0.023 0.002 PHE A 347 TRP 0.035 0.002 TRP A 749 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00319 (11360) covalent geometry : angle 0.73312 (15446) hydrogen bonds : bond 0.03993 ( 377) hydrogen bonds : angle 6.25955 ( 1083) *********************** 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 174 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.404 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 109 MET cc_start: 0.8206 (ttt) cc_final: 0.7930 (tmm) REVERT: A 303 LYS cc_start: 0.8714 (tmmt) cc_final: 0.8425 (tmtt) REVERT: A 368 GLU cc_start: 0.8144 (mm-30) cc_final: 0.6786 (tp30) REVERT: A 396 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 539 MET cc_start: 0.7677 (tpp) cc_final: 0.7172 (tpp) REVERT: A 711 MET cc_start: 0.8621 (ttt) cc_final: 0.8415 (ttt) REVERT: B 63 LEU cc_start: 0.9240 (tp) cc_final: 0.9011 (tp) REVERT: C 83 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8618 (mmt90) REVERT: D 34 GLU cc_start: 0.9625 (tp30) cc_final: 0.9375 (tp30) REVERT: D 109 MET cc_start: 0.6010 (ppp) cc_final: 0.5648 (ppp) REVERT: D 145 SER cc_start: 0.9065 (m) cc_final: 0.8783 (p) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0929 time to fit residues: 23.5218 Evaluate side-chains 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 229 GLN C 34 GLN D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.067026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053444 restraints weight = 67260.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054956 restraints weight = 43639.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056001 restraints weight = 31829.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056711 restraints weight = 25387.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.057234 restraints weight = 21536.679| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11360 Z= 0.164 Angle : 0.756 11.439 15446 Z= 0.393 Chirality : 0.046 0.171 1687 Planarity : 0.005 0.063 2036 Dihedral : 6.477 42.297 1563 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 21.84 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 : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.22), residues: 1416 helix: -0.31 (0.29), residues: 307 sheet: -2.24 (0.27), residues: 354 loop : -2.95 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 366 TYR 0.028 0.002 TYR C 41 PHE 0.021 0.002 PHE A 347 TRP 0.047 0.003 TRP D 191 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00363 (11360) covalent geometry : angle 0.75600 (15446) hydrogen bonds : bond 0.04037 ( 377) hydrogen bonds : angle 6.25589 ( 1083) *********************** 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 158 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8229 (ttt) cc_final: 0.7967 (tmm) REVERT: A 303 LYS cc_start: 0.8634 (tmmt) cc_final: 0.8359 (tmtt) REVERT: A 368 GLU cc_start: 0.8128 (mm-30) cc_final: 0.6726 (tp30) REVERT: A 395 PHE cc_start: 0.5769 (p90) cc_final: 0.5367 (p90) REVERT: A 396 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8072 (tm-30) REVERT: A 512 ASP cc_start: 0.8662 (p0) cc_final: 0.8263 (t0) REVERT: A 539 MET cc_start: 0.7833 (tpp) cc_final: 0.7379 (tpp) REVERT: A 545 MET cc_start: 0.9322 (mtm) cc_final: 0.9106 (mtp) REVERT: A 711 MET cc_start: 0.8676 (ttt) cc_final: 0.8469 (ttt) REVERT: B 63 LEU cc_start: 0.9244 (tp) cc_final: 0.9018 (tp) REVERT: C 83 ARG cc_start: 0.8957 (mmm-85) cc_final: 0.8650 (mmt90) REVERT: D 34 GLU cc_start: 0.9648 (tp30) cc_final: 0.9407 (tp30) REVERT: D 109 MET cc_start: 0.6041 (ppp) cc_final: 0.5712 (ppp) REVERT: D 145 SER cc_start: 0.9058 (m) cc_final: 0.8757 (p) REVERT: E 63 LEU cc_start: 0.8726 (mm) cc_final: 0.8497 (mm) REVERT: E 71 ASN cc_start: 0.7761 (t0) cc_final: 0.7178 (t0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0994 time to fit residues: 22.5254 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 7.9990 chunk 100 optimal weight: 0.0040 chunk 115 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS ** 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 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054655 restraints weight = 68204.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056099 restraints weight = 45305.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.057121 restraints weight = 33555.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.057814 restraints weight = 26898.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.058307 restraints weight = 22898.739| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5586 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= 0.149 Angle : 0.738 11.465 15446 Z= 0.382 Chirality : 0.046 0.168 1687 Planarity : 0.005 0.067 2036 Dihedral : 6.288 41.539 1563 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.65 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.22), residues: 1416 helix: -0.16 (0.29), residues: 307 sheet: -2.17 (0.27), residues: 357 loop : -2.88 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 197 TYR 0.032 0.002 TYR D 79 PHE 0.034 0.002 PHE D 95 TRP 0.035 0.002 TRP D 191 HIS 0.006 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00333 (11360) covalent geometry : angle 0.73814 (15446) hydrogen bonds : bond 0.03979 ( 377) hydrogen bonds : angle 6.01522 ( 1083) ********************** 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 164 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8581 (tmmt) cc_final: 0.8286 (tmtt) REVERT: A 368 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7049 (tp30) REVERT: A 396 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 512 ASP cc_start: 0.8716 (p0) cc_final: 0.8134 (t0) REVERT: A 539 MET cc_start: 0.7940 (tpp) cc_final: 0.7452 (tpp) REVERT: A 545 MET cc_start: 0.9349 (mtm) cc_final: 0.9001 (mtm) REVERT: A 711 MET cc_start: 0.8582 (ttt) cc_final: 0.8371 (ttt) REVERT: B 51 SER cc_start: 0.9249 (m) cc_final: 0.8738 (t) REVERT: B 226 MET cc_start: 0.8583 (ttm) cc_final: 0.8353 (tmm) REVERT: C 56 MET cc_start: 0.7511 (mtt) cc_final: 0.7064 (mtt) REVERT: C 83 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8641 (mmt90) REVERT: D 34 GLU cc_start: 0.9653 (tp30) cc_final: 0.9422 (tp30) REVERT: D 109 MET cc_start: 0.5989 (ppp) cc_final: 0.5690 (ppp) REVERT: D 145 SER cc_start: 0.9067 (m) cc_final: 0.8774 (p) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0920 time to fit residues: 22.3720 Evaluate side-chains 125 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 134 optimal weight: 0.0030 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 overall best weight: 1.2996 ------------------------------------------------------------------------------- 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** C 34 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.068152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054442 restraints weight = 68067.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055902 restraints weight = 44508.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056965 restraints weight = 32807.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.057700 restraints weight = 26266.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.058211 restraints weight = 22215.028| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5754 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= 0.150 Angle : 0.745 12.547 15446 Z= 0.385 Chirality : 0.046 0.198 1687 Planarity : 0.005 0.068 2036 Dihedral : 6.212 41.197 1563 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.79 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.22), residues: 1416 helix: -0.16 (0.28), residues: 309 sheet: -2.12 (0.26), residues: 351 loop : -2.85 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 197 TYR 0.038 0.002 TYR B 263 PHE 0.052 0.002 PHE D 64 TRP 0.034 0.002 TRP D 191 HIS 0.007 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00335 (11360) covalent geometry : angle 0.74496 (15446) hydrogen bonds : bond 0.04011 ( 377) hydrogen bonds : angle 5.97085 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.63 seconds wall clock time: 30 minutes 43.67 seconds (1843.67 seconds total)