Starting phenix.real_space_refine on Thu Feb 5 17:11:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9leo_63031/02_2026/9leo_63031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9leo_63031/02_2026/9leo_63031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9leo_63031/02_2026/9leo_63031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9leo_63031/02_2026/9leo_63031.map" model { file = "/net/cci-nas-00/data/ceres_data/9leo_63031/02_2026/9leo_63031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9leo_63031/02_2026/9leo_63031.cif" } resolution = 2.92 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5930 2.51 5 N 1536 2.21 5 O 1847 1.98 5 H 9056 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18413 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3168 Classifications: {'peptide': 210} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 1 Chain: "B" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2995 Classifications: {'peptide': 196} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 186} Chain: "C" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 2658 Classifications: {'peptide': 174} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Chain: "D" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 2998 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 190} Chain breaks: 3 Chain: "H" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6594 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 405} Time building chain proxies: 3.19, per 1000 atoms: 0.17 Number of scatterers: 18413 At special positions: 0 Unit cell: (171.855, 106.875, 72.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1847 8.00 N 1536 7.00 C 5930 6.00 H 9056 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 188 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 219 " - pdb=" SG CYS H 243 " distance=2.03 Simple disulfide: pdb=" SG CYS H 285 " - pdb=" SG CYS H 298 " distance=2.03 Simple disulfide: pdb=" SG CYS H 379 " - pdb=" SG CYS H 396 " distance=2.03 Simple disulfide: pdb=" SG CYS H 384 " - pdb=" SG CYS H 502 " distance=2.02 Simple disulfide: pdb=" SG CYS H 494 " - pdb=" SG CYS H 506 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 577 " distance=2.03 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: 1.53 Conformation dependent library (CDL) restraints added in 656.5 milliseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 27 sheets defined 5.9% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.564A pdb=" N THR A 91 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.676A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.511A pdb=" N GLY B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'C' and resid 62 through 66 removed outlier: 6.516A pdb=" N SER C 66 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.574A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 393 through 400 removed outlier: 3.815A pdb=" N VAL H 400 " --> pdb=" O CYS H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 437 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.554A pdb=" N ALA A 92 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP A 35 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER A 51 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP A 37 " --> pdb=" O MET A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.693A pdb=" N SER A 184 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 176 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.507A pdb=" N THR A 158 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 206 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.500A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP B 70 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118 removed outlier: 5.390A pdb=" N SER B 131 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 181 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 133 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 179 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.523A pdb=" N THR C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 18 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 83 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.411A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.629A pdb=" N LYS C 149 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.044A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 67 " --> pdb=" O GLN D 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 65 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.281A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS D 107 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA D 13 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 129 through 139 removed outlier: 3.760A pdb=" N SER D 177 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 154 through 155 removed outlier: 4.716A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 177 through 178 removed outlier: 6.890A pdb=" N GLU H 582 " --> pdb=" O THR H 562 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 564 " --> pdb=" O VAL H 580 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL H 580 " --> pdb=" O ALA H 564 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE H 566 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE H 578 " --> pdb=" O ILE H 566 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS H 568 " --> pdb=" O TRP H 576 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 576 " --> pdb=" O CYS H 568 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE H 575 " --> pdb=" O VAL H 600 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET H 603 " --> pdb=" O THR H 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 177 through 178 removed outlier: 6.890A pdb=" N GLU H 582 " --> pdb=" O THR H 562 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 564 " --> pdb=" O VAL H 580 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL H 580 " --> pdb=" O ALA H 564 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE H 566 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE H 578 " --> pdb=" O ILE H 566 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS H 568 " --> pdb=" O TRP H 576 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 576 " --> pdb=" O CYS H 568 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE H 575 " --> pdb=" O VAL H 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 219 through 220 Processing sheet with id=AC4, first strand: chain 'H' and resid 219 through 220 removed outlier: 3.722A pdb=" N SER H 250 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG H 257 " --> pdb=" O PRO H 270 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 282 through 289 removed outlier: 6.851A pdb=" N SER H 299 " --> pdb=" O ASN H 283 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS H 285 " --> pdb=" O LEU H 297 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU H 297 " --> pdb=" O CYS H 285 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL H 287 " --> pdb=" O TRP H 295 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP H 295 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 300 " --> pdb=" O GLY H 316 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY H 316 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU H 323 " --> pdb=" O GLU H 327 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 338 through 339 removed outlier: 3.870A pdb=" N SER H 429 " --> pdb=" O LEU H 339 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 426 " --> pdb=" O ASN H 418 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR H 362 " --> pdb=" O ILE H 355 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 344 through 349 removed outlier: 7.323A pdb=" N TYR H 344 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG H 370 " --> pdb=" O TYR H 344 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER H 346 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER H 408 " --> pdb=" O SER H 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 443 through 446 Processing sheet with id=AC9, first strand: chain 'H' and resid 515 through 516 removed outlier: 4.766A pdb=" N SER H 538 " --> pdb=" O ILE H 554 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE H 554 " --> pdb=" O SER H 538 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA H 550 " --> pdb=" O VAL H 542 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9055 1.03 - 1.23: 62 1.23 - 1.43: 4077 1.43 - 1.62: 5389 1.62 - 1.82: 59 Bond restraints: 18642 Sorted by residual: bond pdb=" C LYS H 537 " pdb=" O LYS H 537 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.20e-02 6.94e+03 1.60e+01 bond pdb=" CA SER D 162 " pdb=" CB SER D 162 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.38e-02 5.25e+03 1.42e+01 bond pdb=" C VAL C 86 " pdb=" O VAL C 86 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N GLN H 198 " pdb=" CA GLN H 198 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.11e+01 bond pdb=" N VAL A 2 " pdb=" CA VAL A 2 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.27e-02 6.20e+03 1.11e+01 ... (remaining 18637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 32074 2.13 - 4.25: 1331 4.25 - 6.38: 131 6.38 - 8.51: 17 8.51 - 10.64: 6 Bond angle restraints: 33559 Sorted by residual: angle pdb=" C TYR C 182 " pdb=" CA TYR C 182 " pdb=" CB TYR C 182 " ideal model delta sigma weight residual 109.80 101.24 8.56 1.23e+00 6.61e-01 4.85e+01 angle pdb=" CA TRP A 37 " pdb=" C TRP A 37 " pdb=" O TRP A 37 " ideal model delta sigma weight residual 120.36 113.41 6.95 1.08e+00 8.57e-01 4.14e+01 angle pdb=" CA ASP A 108 " pdb=" CB ASP A 108 " pdb=" CG ASP A 108 " ideal model delta sigma weight residual 112.60 118.81 -6.21 1.00e+00 1.00e+00 3.86e+01 angle pdb=" CA ASP H 498 " pdb=" CB ASP H 498 " pdb=" CG ASP H 498 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" N GLY A 43 " pdb=" CA GLY A 43 " pdb=" C GLY A 43 " ideal model delta sigma weight residual 114.92 107.20 7.72 1.30e+00 5.92e-01 3.52e+01 ... (remaining 33554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 7958 21.10 - 42.19: 733 42.19 - 63.29: 240 63.29 - 84.38: 54 84.38 - 105.48: 11 Dihedral angle restraints: 8996 sinusoidal: 4793 harmonic: 4203 Sorted by residual: dihedral pdb=" CA PHE C 152 " pdb=" C PHE C 152 " pdb=" N PRO C 153 " pdb=" CA PRO C 153 " ideal model delta harmonic sigma weight residual -180.00 -74.52 -105.48 0 5.00e+00 4.00e-02 4.45e+02 dihedral pdb=" CD ARG H 372 " pdb=" NE ARG H 372 " pdb=" CZ ARG H 372 " pdb=" NH1 ARG H 372 " ideal model delta sinusoidal sigma weight residual 0.00 -87.26 87.26 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CD ARG A 72 " pdb=" NE ARG A 72 " pdb=" CZ ARG A 72 " pdb=" NH1 ARG A 72 " ideal model delta sinusoidal sigma weight residual 0.00 -79.37 79.37 1 1.00e+01 1.00e-02 7.83e+01 ... (remaining 8993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1174 0.070 - 0.140: 226 0.140 - 0.210: 45 0.210 - 0.280: 4 0.280 - 0.350: 3 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA PRO C 103 " pdb=" N PRO C 103 " pdb=" C PRO C 103 " pdb=" CB PRO C 103 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ILE A 57 " pdb=" N ILE A 57 " pdb=" C ILE A 57 " pdb=" CB ILE A 57 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA ILE H 355 " pdb=" N ILE H 355 " pdb=" C ILE H 355 " pdb=" CB ILE H 355 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1449 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 18 " -0.488 9.50e-02 1.11e+02 5.17e-01 5.44e+03 pdb=" NE ARG B 18 " 0.260 2.00e-02 2.50e+03 pdb=" CZ ARG B 18 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG B 18 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG B 18 " -0.036 2.00e-02 2.50e+03 pdb="HH11 ARG B 18 " 0.658 2.00e-02 2.50e+03 pdb="HH12 ARG B 18 " -0.766 2.00e-02 2.50e+03 pdb="HH21 ARG B 18 " -0.805 2.00e-02 2.50e+03 pdb="HH22 ARG B 18 " 0.651 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 72 " 1.431 9.50e-02 1.11e+02 6.72e-01 5.26e+03 pdb=" NE ARG C 72 " 0.147 2.00e-02 2.50e+03 pdb=" CZ ARG C 72 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 72 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 72 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG C 72 " -0.676 2.00e-02 2.50e+03 pdb="HH12 ARG C 72 " 0.643 2.00e-02 2.50e+03 pdb="HH21 ARG C 72 " 0.676 2.00e-02 2.50e+03 pdb="HH22 ARG C 72 " -0.812 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 451 " -1.337 9.50e-02 1.11e+02 6.43e-01 5.03e+03 pdb=" NE ARG H 451 " -0.138 2.00e-02 2.50e+03 pdb=" CZ ARG H 451 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG H 451 " 0.057 2.00e-02 2.50e+03 pdb=" NH2 ARG H 451 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG H 451 " -0.655 2.00e-02 2.50e+03 pdb="HH12 ARG H 451 " 0.834 2.00e-02 2.50e+03 pdb="HH21 ARG H 451 " 0.632 2.00e-02 2.50e+03 pdb="HH22 ARG H 451 " -0.622 2.00e-02 2.50e+03 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2418 2.24 - 2.83: 39582 2.83 - 3.42: 47529 3.42 - 4.01: 67158 4.01 - 4.60: 97981 Nonbonded interactions: 254668 Sorted by model distance: nonbonded pdb="HE22 GLN D 6 " pdb=" O TYR D 86 " model vdw 1.648 2.450 nonbonded pdb=" OE1 GLN D 40 " pdb=" H GLN D 40 " model vdw 1.649 2.450 nonbonded pdb=" O GLY D 68 " pdb=" HH TYR D 71 " model vdw 1.656 2.450 nonbonded pdb=" OD2 ASP H 242 " pdb=" HG1 THR H 245 " model vdw 1.678 2.450 nonbonded pdb=" OE1 GLU B 165 " pdb=" H GLU B 165 " model vdw 1.678 2.450 ... (remaining 254663 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 individual isotropic 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: 1.740 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: 0.110 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.290 Find NCS groups from input model: 0.080 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:9.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.007 0.052 9600 Z= 0.472 Angle : 1.129 10.636 13062 Z= 0.764 Chirality : 0.061 0.350 1452 Planarity : 0.033 0.501 1660 Dihedral : 17.162 105.481 3424 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.80 % Favored : 93.87 % Rotamer: Outliers : 5.20 % Allowed : 20.79 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % 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: -1.57 (0.25), residues: 1190 helix: -1.42 (0.82), residues: 31 sheet: -0.48 (0.24), residues: 487 loop : -1.46 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 142 TYR 0.026 0.002 TYR C 51 PHE 0.016 0.001 PHE A 80 TRP 0.012 0.001 TRP A 110 HIS 0.004 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 9586) covalent geometry : angle 1.12942 (13034) SS BOND : bond 0.00317 ( 14) SS BOND : angle 0.69369 ( 28) hydrogen bonds : bond 0.26744 ( 288) hydrogen bonds : angle 10.61450 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.443 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 10 ASP cc_start: 0.8759 (p0) cc_final: 0.8557 (p0) REVERT: A 89 GLU cc_start: 0.8794 (mp0) cc_final: 0.8591 (mp0) REVERT: A 151 ASP cc_start: 0.8897 (m-30) cc_final: 0.8589 (m-30) REVERT: A 199 GLN cc_start: 0.9266 (mm110) cc_final: 0.8902 (mm-40) REVERT: B 81 GLU cc_start: 0.8661 (pm20) cc_final: 0.8428 (pm20) REVERT: C 89 GLU cc_start: 0.8817 (tp30) cc_final: 0.8445 (tp30) REVERT: C 111 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: D 79 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.7776 (t70) REVERT: H 419 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7467 (p0) REVERT: H 505 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8250 (pp) outliers start: 55 outliers final: 14 residues processed: 143 average time/residue: 1.2775 time to fit residues: 194.8634 Evaluate side-chains 89 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN C 78 GLN C 84 ASN C 161 ASN D 34 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 371 ASN H 557 ASN H 586 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.087972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064758 restraints weight = 85930.702| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.24 r_work: 0.3117 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9600 Z= 0.161 Angle : 0.620 6.326 13062 Z= 0.327 Chirality : 0.044 0.163 1452 Planarity : 0.008 0.147 1660 Dihedral : 7.211 61.723 1342 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 3.40 % Allowed : 21.83 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -1.22 (0.25), residues: 1190 helix: 0.01 (0.93), residues: 31 sheet: -0.23 (0.24), residues: 501 loop : -1.32 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 451 TYR 0.013 0.001 TYR C 51 PHE 0.019 0.002 PHE C 152 TRP 0.010 0.001 TRP C 35 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9586) covalent geometry : angle 0.62014 (13034) SS BOND : bond 0.00274 ( 14) SS BOND : angle 0.67552 ( 28) hydrogen bonds : bond 0.04320 ( 288) hydrogen bonds : angle 7.00420 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.685 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 89 GLU cc_start: 0.8756 (mp0) cc_final: 0.8548 (mp0) REVERT: A 129 PHE cc_start: 0.8585 (m-10) cc_final: 0.8347 (m-80) REVERT: A 151 ASP cc_start: 0.9106 (m-30) cc_final: 0.8764 (m-30) REVERT: A 199 GLN cc_start: 0.9289 (mm110) cc_final: 0.8933 (mm-40) REVERT: B 81 GLU cc_start: 0.8858 (pm20) cc_final: 0.8547 (pm20) REVERT: B 82 ASP cc_start: 0.8340 (m-30) cc_final: 0.7916 (m-30) REVERT: C 89 GLU cc_start: 0.8902 (tp30) cc_final: 0.8527 (tp30) REVERT: D 58 MET cc_start: 0.8816 (mmm) cc_final: 0.8242 (mmt) REVERT: D 79 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8029 (t70) REVERT: H 364 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: H 505 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8096 (pp) outliers start: 36 outliers final: 20 residues processed: 104 average time/residue: 1.3338 time to fit residues: 148.5111 Evaluate side-chains 92 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 527 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain H residue 605 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.080654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058643 restraints weight = 90155.486| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.98 r_work: 0.3147 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9600 Z= 0.112 Angle : 0.561 5.997 13062 Z= 0.290 Chirality : 0.043 0.157 1452 Planarity : 0.006 0.128 1660 Dihedral : 6.238 62.215 1327 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.84 % Allowed : 21.64 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.92 (0.25), residues: 1190 helix: 0.56 (0.94), residues: 31 sheet: -0.02 (0.24), residues: 499 loop : -1.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 142 TYR 0.012 0.001 TYR C 105 PHE 0.015 0.001 PHE C 152 TRP 0.008 0.001 TRP H 274 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9586) covalent geometry : angle 0.56070 (13034) SS BOND : bond 0.00227 ( 14) SS BOND : angle 0.53407 ( 28) hydrogen bonds : bond 0.03365 ( 288) hydrogen bonds : angle 6.24196 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.521 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 10 ASP cc_start: 0.8819 (p0) cc_final: 0.8603 (p0) REVERT: A 151 ASP cc_start: 0.9008 (m-30) cc_final: 0.8704 (m-30) REVERT: B 81 GLU cc_start: 0.8804 (pm20) cc_final: 0.8473 (pm20) REVERT: B 82 ASP cc_start: 0.8291 (m-30) cc_final: 0.7872 (m-30) REVERT: C 89 GLU cc_start: 0.8905 (tp30) cc_final: 0.8531 (tp30) REVERT: D 58 MET cc_start: 0.8823 (mmm) cc_final: 0.8331 (mmt) REVERT: D 79 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8035 (t70) REVERT: H 364 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: H 505 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8073 (pp) outliers start: 30 outliers final: 15 residues processed: 102 average time/residue: 1.1075 time to fit residues: 121.5073 Evaluate side-chains 86 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 605 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.079254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057282 restraints weight = 91476.876| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.97 r_work: 0.3108 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9600 Z= 0.164 Angle : 0.567 6.438 13062 Z= 0.294 Chirality : 0.043 0.162 1452 Planarity : 0.006 0.132 1660 Dihedral : 5.936 59.786 1320 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.74 % Allowed : 21.36 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.98 (0.25), residues: 1190 helix: 0.80 (0.97), residues: 31 sheet: -0.04 (0.23), residues: 501 loop : -1.21 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.013 0.001 TYR C 51 PHE 0.012 0.001 PHE A 79 TRP 0.009 0.001 TRP H 274 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9586) covalent geometry : angle 0.56745 (13034) SS BOND : bond 0.00235 ( 14) SS BOND : angle 0.54296 ( 28) hydrogen bonds : bond 0.03228 ( 288) hydrogen bonds : angle 5.92989 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.565 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 10 ASP cc_start: 0.8859 (p0) cc_final: 0.8634 (p0) REVERT: A 151 ASP cc_start: 0.9091 (m-30) cc_final: 0.8790 (m-30) REVERT: B 81 GLU cc_start: 0.8850 (pm20) cc_final: 0.8553 (pm20) REVERT: B 82 ASP cc_start: 0.8436 (m-30) cc_final: 0.7972 (m-30) REVERT: C 89 GLU cc_start: 0.8907 (tp30) cc_final: 0.8521 (tp30) REVERT: D 79 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8089 (t70) REVERT: H 364 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: H 505 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8117 (pp) outliers start: 29 outliers final: 21 residues processed: 93 average time/residue: 1.0966 time to fit residues: 109.6855 Evaluate side-chains 92 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 499 LYS Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 527 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain H residue 605 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058314 restraints weight = 89607.976| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.95 r_work: 0.3140 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9600 Z= 0.106 Angle : 0.543 6.198 13062 Z= 0.280 Chirality : 0.043 0.152 1452 Planarity : 0.005 0.129 1660 Dihedral : 5.795 60.052 1320 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.08 % Allowed : 22.02 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.80 (0.25), residues: 1190 helix: 1.01 (0.99), residues: 31 sheet: 0.07 (0.23), residues: 502 loop : -1.09 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 142 TYR 0.014 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.008 0.001 TRP H 274 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9586) covalent geometry : angle 0.54355 (13034) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.50539 ( 28) hydrogen bonds : bond 0.02812 ( 288) hydrogen bonds : angle 5.60410 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.571 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 10 ASP cc_start: 0.8888 (p0) cc_final: 0.8627 (p0) REVERT: A 151 ASP cc_start: 0.9027 (m-30) cc_final: 0.8730 (m-30) REVERT: A 199 GLN cc_start: 0.9310 (mm110) cc_final: 0.8959 (mm110) REVERT: B 81 GLU cc_start: 0.8845 (pm20) cc_final: 0.8532 (pm20) REVERT: B 82 ASP cc_start: 0.8370 (m-30) cc_final: 0.7913 (m-30) REVERT: B 155 GLN cc_start: 0.8427 (mp10) cc_final: 0.6738 (pm20) REVERT: B 165 GLU cc_start: 0.8324 (tp30) cc_final: 0.8079 (tp30) REVERT: C 89 GLU cc_start: 0.8888 (tp30) cc_final: 0.8515 (tp30) REVERT: C 181 LEU cc_start: 0.8454 (mt) cc_final: 0.8200 (mt) REVERT: D 79 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8114 (t70) REVERT: H 505 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8117 (pp) outliers start: 22 outliers final: 14 residues processed: 89 average time/residue: 1.0620 time to fit residues: 101.6793 Evaluate side-chains 84 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.078384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056683 restraints weight = 91467.647| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.94 r_work: 0.3089 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9600 Z= 0.192 Angle : 0.568 6.356 13062 Z= 0.296 Chirality : 0.043 0.156 1452 Planarity : 0.005 0.133 1660 Dihedral : 5.676 58.502 1315 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.93 % Allowed : 21.27 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.99 (0.24), residues: 1190 helix: 0.91 (0.95), residues: 31 sheet: -0.03 (0.23), residues: 500 loop : -1.24 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 142 TYR 0.016 0.002 TYR C 51 PHE 0.013 0.001 PHE C 79 TRP 0.009 0.001 TRP H 274 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9586) covalent geometry : angle 0.56832 (13034) SS BOND : bond 0.00235 ( 14) SS BOND : angle 0.59189 ( 28) hydrogen bonds : bond 0.03207 ( 288) hydrogen bonds : angle 5.64463 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.640 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 10 ASP cc_start: 0.8924 (p0) cc_final: 0.8710 (p0) REVERT: A 151 ASP cc_start: 0.9166 (m-30) cc_final: 0.8865 (m-30) REVERT: B 81 GLU cc_start: 0.8891 (pm20) cc_final: 0.8566 (pm20) REVERT: B 82 ASP cc_start: 0.8490 (m-30) cc_final: 0.8029 (m-30) REVERT: C 89 GLU cc_start: 0.8898 (tp30) cc_final: 0.8520 (tp30) REVERT: D 79 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.8106 (t70) REVERT: H 267 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: H 364 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7964 (tm-30) outliers start: 31 outliers final: 21 residues processed: 93 average time/residue: 1.1521 time to fit residues: 115.2943 Evaluate side-chains 87 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 267 GLN Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 527 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain H residue 605 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057979 restraints weight = 90178.226| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.95 r_work: 0.3125 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9600 Z= 0.105 Angle : 0.553 7.396 13062 Z= 0.285 Chirality : 0.043 0.149 1452 Planarity : 0.005 0.129 1660 Dihedral : 5.544 59.705 1311 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.89 % Allowed : 22.87 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.77 (0.25), residues: 1190 helix: 1.26 (0.98), residues: 31 sheet: 0.07 (0.23), residues: 502 loop : -1.07 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 142 TYR 0.015 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.010 0.001 TRP H 274 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9586) covalent geometry : angle 0.55330 (13034) SS BOND : bond 0.00200 ( 14) SS BOND : angle 0.50275 ( 28) hydrogen bonds : bond 0.02712 ( 288) hydrogen bonds : angle 5.39210 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8907 (p0) cc_final: 0.8664 (p0) REVERT: A 151 ASP cc_start: 0.9098 (m-30) cc_final: 0.8796 (m-30) REVERT: A 199 GLN cc_start: 0.9314 (mm110) cc_final: 0.8957 (mm-40) REVERT: B 81 GLU cc_start: 0.8797 (pm20) cc_final: 0.8482 (pm20) REVERT: B 82 ASP cc_start: 0.8412 (m-30) cc_final: 0.7975 (m-30) REVERT: B 165 GLU cc_start: 0.8243 (tp30) cc_final: 0.8040 (tp30) REVERT: C 89 GLU cc_start: 0.8863 (tp30) cc_final: 0.8480 (tp30) REVERT: C 181 LEU cc_start: 0.8533 (mt) cc_final: 0.8276 (mt) REVERT: D 79 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.8127 (t70) REVERT: D 143 GLU cc_start: 0.8786 (mp0) cc_final: 0.8436 (pm20) REVERT: H 267 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: H 364 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: H 488 MET cc_start: 0.8091 (tpp) cc_final: 0.7768 (tpp) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 1.2997 time to fit residues: 122.4255 Evaluate side-chains 79 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 267 GLN Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 97 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.078871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057137 restraints weight = 90895.956| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.95 r_work: 0.3105 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9600 Z= 0.146 Angle : 0.566 7.556 13062 Z= 0.293 Chirality : 0.043 0.151 1452 Planarity : 0.005 0.132 1660 Dihedral : 5.536 58.049 1311 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.80 % Allowed : 23.25 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.81 (0.25), residues: 1190 helix: 1.24 (0.98), residues: 31 sheet: 0.09 (0.23), residues: 506 loop : -1.14 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 142 TYR 0.012 0.001 TYR C 51 PHE 0.010 0.001 PHE C 79 TRP 0.008 0.001 TRP H 274 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9586) covalent geometry : angle 0.56632 (13034) SS BOND : bond 0.00234 ( 14) SS BOND : angle 0.51093 ( 28) hydrogen bonds : bond 0.02921 ( 288) hydrogen bonds : angle 5.34023 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8911 (p0) cc_final: 0.8665 (p0) REVERT: A 131 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7592 (mm) REVERT: A 151 ASP cc_start: 0.9133 (m-30) cc_final: 0.8846 (m-30) REVERT: B 81 GLU cc_start: 0.8850 (pm20) cc_final: 0.8532 (pm20) REVERT: B 82 ASP cc_start: 0.8484 (m-30) cc_final: 0.8072 (m-30) REVERT: C 89 GLU cc_start: 0.8866 (tp30) cc_final: 0.8443 (tm-30) REVERT: D 79 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8134 (t70) REVERT: D 143 GLU cc_start: 0.8898 (mp0) cc_final: 0.8627 (pm20) REVERT: H 267 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: H 364 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8020 (tm-30) outliers start: 19 outliers final: 14 residues processed: 84 average time/residue: 1.1791 time to fit residues: 106.3472 Evaluate side-chains 82 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 267 GLN Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 101 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.084976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.062742 restraints weight = 88409.156| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.14 r_work: 0.3087 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9600 Z= 0.167 Angle : 0.585 8.079 13062 Z= 0.303 Chirality : 0.043 0.154 1452 Planarity : 0.006 0.134 1660 Dihedral : 5.664 58.829 1311 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.98 % Allowed : 23.44 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.88 (0.25), residues: 1190 helix: 1.07 (0.96), residues: 31 sheet: 0.04 (0.23), residues: 502 loop : -1.18 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 142 TYR 0.023 0.001 TYR B 186 PHE 0.011 0.001 PHE C 79 TRP 0.009 0.001 TRP H 274 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9586) covalent geometry : angle 0.58487 (13034) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.59156 ( 28) hydrogen bonds : bond 0.02994 ( 288) hydrogen bonds : angle 5.35760 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8917 (p0) cc_final: 0.8659 (p0) REVERT: A 129 PHE cc_start: 0.8547 (m-10) cc_final: 0.8120 (m-80) REVERT: A 151 ASP cc_start: 0.9130 (m-30) cc_final: 0.8849 (m-30) REVERT: B 81 GLU cc_start: 0.8832 (pm20) cc_final: 0.8509 (pm20) REVERT: B 82 ASP cc_start: 0.8533 (m-30) cc_final: 0.8060 (m-30) REVERT: C 16 GLN cc_start: 0.8321 (mm110) cc_final: 0.8066 (mm110) REVERT: C 89 GLU cc_start: 0.8871 (tp30) cc_final: 0.8462 (tm-30) REVERT: D 79 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8144 (t70) REVERT: H 267 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: H 364 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7979 (tm-30) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 1.2304 time to fit residues: 113.9966 Evaluate side-chains 82 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 267 GLN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain H residue 605 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.085631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063128 restraints weight = 87339.906| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.21 r_work: 0.3091 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9600 Z= 0.147 Angle : 0.584 9.226 13062 Z= 0.301 Chirality : 0.043 0.156 1452 Planarity : 0.005 0.133 1660 Dihedral : 5.647 58.415 1311 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.89 % Allowed : 23.72 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.84 (0.25), residues: 1190 helix: 1.04 (0.95), residues: 31 sheet: 0.10 (0.23), residues: 510 loop : -1.18 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 142 TYR 0.012 0.001 TYR B 92 PHE 0.010 0.001 PHE A 79 TRP 0.009 0.001 TRP H 274 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9586) covalent geometry : angle 0.58408 (13034) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.55230 ( 28) hydrogen bonds : bond 0.02877 ( 288) hydrogen bonds : angle 5.28224 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8948 (p0) cc_final: 0.8681 (p0) REVERT: A 129 PHE cc_start: 0.8545 (m-10) cc_final: 0.8318 (m-80) REVERT: A 151 ASP cc_start: 0.9160 (m-30) cc_final: 0.8883 (m-30) REVERT: A 216 LYS cc_start: 0.8301 (tptm) cc_final: 0.8036 (tppp) REVERT: B 81 GLU cc_start: 0.8861 (pm20) cc_final: 0.8524 (pm20) REVERT: B 82 ASP cc_start: 0.8476 (m-30) cc_final: 0.8066 (m-30) REVERT: C 16 GLN cc_start: 0.8285 (mm110) cc_final: 0.8032 (mm110) REVERT: C 89 GLU cc_start: 0.8858 (tp30) cc_final: 0.8445 (tm-30) REVERT: D 79 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8170 (t70) REVERT: H 267 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: H 364 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: H 488 MET cc_start: 0.8136 (tpp) cc_final: 0.7897 (tpp) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 1.2996 time to fit residues: 124.2404 Evaluate side-chains 81 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 267 GLN Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 504 GLU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 538 SER Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain H residue 605 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN H 393 GLN H 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.079456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.057680 restraints weight = 90381.508| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.94 r_work: 0.3118 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9600 Z= 0.112 Angle : 0.584 8.778 13062 Z= 0.300 Chirality : 0.043 0.166 1452 Planarity : 0.005 0.132 1660 Dihedral : 5.577 58.754 1311 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.80 % Allowed : 23.91 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % 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: -0.72 (0.25), residues: 1190 helix: 1.22 (0.97), residues: 31 sheet: 0.17 (0.23), residues: 508 loop : -1.09 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 142 TYR 0.022 0.001 TYR B 186 PHE 0.010 0.001 PHE C 152 TRP 0.010 0.001 TRP H 274 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9586) covalent geometry : angle 0.58427 (13034) SS BOND : bond 0.00201 ( 14) SS BOND : angle 0.51778 ( 28) hydrogen bonds : bond 0.02665 ( 288) hydrogen bonds : angle 5.15927 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.64 seconds wall clock time: 103 minutes 0.62 seconds (6180.62 seconds total)