Starting phenix.real_space_refine on Wed Feb 4 07:54:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkx_62397/02_2026/9kkx_62397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkx_62397/02_2026/9kkx_62397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kkx_62397/02_2026/9kkx_62397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkx_62397/02_2026/9kkx_62397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kkx_62397/02_2026/9kkx_62397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkx_62397/02_2026/9kkx_62397.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5866 2.51 5 N 1608 2.21 5 O 1754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 9291 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1138 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain breaks: 1 Chain: "B" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1045 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Chain: "A" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2094 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 15, 'TRANS': 253} Chain: "C" Number of atoms: 5007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5007 Classifications: {'peptide': 641} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 608} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'GR2': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GR2:plan-1': 1, 'GR2:plan-2': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9291 At special positions: 0 Unit cell: (75.92, 113.88, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1754 8.00 N 1608 7.00 C 5866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 391.2 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 51.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'D' and resid 13 through 31 Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.704A pdb=" N VAL D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 4.441A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS D 60 " --> pdb=" O CYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 65 through 81 removed outlier: 3.992A pdb=" N CYS D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 79 " --> pdb=" O CYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 114 Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 140 through 150 removed outlier: 3.738A pdb=" N GLU D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 150 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 removed outlier: 3.701A pdb=" N ASN D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.840A pdb=" N SER B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 48 through 64 removed outlier: 4.848A pdb=" N GLU B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.510A pdb=" N MET B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.642A pdb=" N SER A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.196A pdb=" N TYR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.644A pdb=" N GLU A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.692A pdb=" N PHE A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.076A pdb=" N GLY A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.966A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 252 through 266 Proline residue: A 258 - end of helix Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.801A pdb=" N ILE C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.617A pdb=" N ILE C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 176 through 181 removed outlier: 3.599A pdb=" N LEU C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 209 Processing helix chain 'C' and resid 211 through 218 removed outlier: 3.635A pdb=" N LEU C 218 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 288 through 291 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.167A pdb=" N PHE C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.613A pdb=" N ASN C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 457 through 460 Processing helix chain 'C' and resid 547 through 553 removed outlier: 4.437A pdb=" N ALA C 551 " --> pdb=" O THR C 547 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.909A pdb=" N TRP C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.663A pdb=" N GLU C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 681 through 685 Processing helix chain 'C' and resid 710 through 723 Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.619A pdb=" N THR A 19 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 92 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 21 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 89 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 116 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 91 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N HIS A 210 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU A 115 " --> pdb=" O HIS A 210 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 212 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET A 117 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N SER A 214 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.558A pdb=" N LEU C 138 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 164 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 140 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 161 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU C 194 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 163 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 196 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS C 335 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE C 363 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N ASN C 336 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 469 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 466 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TRP C 539 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 468 " --> pdb=" O TRP C 539 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N PHE C 541 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY C 601 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLY C 569 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 603 " --> pdb=" O GLY C 569 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1568 1.31 - 1.44: 2360 1.44 - 1.56: 5453 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 9473 Sorted by residual: bond pdb=" C14 GR2 A 301 " pdb=" C15 GR2 A 301 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C16 GR2 A 301 " pdb=" O5 GR2 A 301 " ideal model delta sigma weight residual 1.350 1.419 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C13 GR2 A 301 " pdb=" O5 GR2 A 301 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.44e+00 bond pdb=" N SER C 184 " pdb=" CA SER C 184 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.15e-02 7.56e+03 6.29e+00 bond pdb=" N CYS C 186 " pdb=" CA CYS C 186 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.80e+00 ... (remaining 9468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 12402 1.12 - 2.24: 325 2.24 - 3.36: 92 3.36 - 4.47: 27 4.47 - 5.59: 9 Bond angle restraints: 12855 Sorted by residual: angle pdb=" N THR C 188 " pdb=" CA THR C 188 " pdb=" C THR C 188 " ideal model delta sigma weight residual 112.03 106.49 5.54 1.31e+00 5.83e-01 1.79e+01 angle pdb=" CA ARG C 724 " pdb=" C ARG C 724 " pdb=" O ARG C 724 " ideal model delta sigma weight residual 121.16 117.06 4.10 1.12e+00 7.97e-01 1.34e+01 angle pdb=" CA GLY C 187 " pdb=" C GLY C 187 " pdb=" O GLY C 187 " ideal model delta sigma weight residual 121.90 118.31 3.59 1.08e+00 8.57e-01 1.10e+01 angle pdb=" N CYS C 186 " pdb=" CA CYS C 186 " pdb=" C CYS C 186 " ideal model delta sigma weight residual 112.93 109.25 3.68 1.12e+00 7.97e-01 1.08e+01 angle pdb=" N ARG C 724 " pdb=" CA ARG C 724 " pdb=" C ARG C 724 " ideal model delta sigma weight residual 110.28 105.69 4.59 1.48e+00 4.57e-01 9.60e+00 ... (remaining 12850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5449 17.83 - 35.65: 246 35.65 - 53.48: 72 53.48 - 71.30: 14 71.30 - 89.13: 3 Dihedral angle restraints: 5784 sinusoidal: 2316 harmonic: 3468 Sorted by residual: dihedral pdb=" CD ARG C 723 " pdb=" NE ARG C 723 " pdb=" CZ ARG C 723 " pdb=" NH1 ARG C 723 " ideal model delta sinusoidal sigma weight residual 0.00 33.27 -33.27 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CA PHE C 89 " pdb=" C PHE C 89 " pdb=" N MET C 90 " pdb=" CA MET C 90 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU C 621 " pdb=" CG GLU C 621 " pdb=" CD GLU C 621 " pdb=" OE1 GLU C 621 " ideal model delta sinusoidal sigma weight residual 0.00 -89.13 89.13 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 960 0.034 - 0.067: 350 0.067 - 0.101: 124 0.101 - 0.134: 47 0.134 - 0.168: 4 Chirality restraints: 1485 Sorted by residual: chirality pdb=" CA GLU C 185 " pdb=" N GLU C 185 " pdb=" C GLU C 185 " pdb=" CB GLU C 185 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CG LEU C 721 " pdb=" CB LEU C 721 " pdb=" CD1 LEU C 721 " pdb=" CD2 LEU C 721 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA THR C 547 " pdb=" N THR C 547 " pdb=" C THR C 547 " pdb=" CB THR C 547 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1482 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 723 " 0.605 9.50e-02 1.11e+02 2.71e-01 4.49e+01 pdb=" NE ARG C 723 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 723 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 723 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 723 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 724 " 0.220 9.50e-02 1.11e+02 9.86e-02 5.97e+00 pdb=" NE ARG C 724 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 724 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 724 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 724 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 720 " -0.010 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ALA C 720 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA C 720 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 721 " -0.011 2.00e-02 2.50e+03 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2232 2.79 - 3.32: 9020 3.32 - 3.85: 15526 3.85 - 4.37: 18988 4.37 - 4.90: 31861 Nonbonded interactions: 77627 Sorted by model distance: nonbonded pdb=" OD1 ASN B 155 " pdb=" NH2 ARG C 73 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR A 67 " pdb=" OD2 ASP A 76 " model vdw 2.270 3.040 nonbonded pdb=" O GLY C 448 " pdb=" OG SER C 452 " model vdw 2.272 3.040 nonbonded pdb=" O PRO D 14 " pdb=" OG1 THR D 18 " model vdw 2.286 3.040 nonbonded pdb=" OE1 GLU A 239 " pdb=" NE2 HIS A 263 " model vdw 2.303 3.120 ... (remaining 77622 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.990 Find NCS groups from input model: 0.060 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:9.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 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 : 0.004 0.116 9474 Z= 0.203 Angle : 0.524 5.593 12855 Z= 0.282 Chirality : 0.042 0.168 1485 Planarity : 0.008 0.271 1659 Dihedral : 11.789 89.131 3528 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.16 % Allowed : 5.81 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.56 (0.25), residues: 1175 helix: 0.79 (0.24), residues: 532 sheet: 0.10 (0.42), residues: 174 loop : 0.19 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 576 TYR 0.007 0.001 TYR C 198 PHE 0.011 0.001 PHE A 84 TRP 0.008 0.001 TRP C 620 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9473) covalent geometry : angle 0.52444 (12855) hydrogen bonds : bond 0.16895 ( 419) hydrogen bonds : angle 6.25101 ( 1164) Misc. bond : bond 0.00590 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: D 111 GLN cc_start: 0.8377 (tp-100) cc_final: 0.8129 (mm-40) REVERT: D 132 GLN cc_start: 0.9190 (mm110) cc_final: 0.8489 (mp10) REVERT: A 140 ASP cc_start: 0.8807 (m-30) cc_final: 0.8488 (m-30) REVERT: A 180 ASN cc_start: 0.9049 (t0) cc_final: 0.8263 (t0) REVERT: C 54 ASP cc_start: 0.8032 (t70) cc_final: 0.7742 (t0) REVERT: C 230 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: C 248 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8151 (ttp80) outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 0.6806 time to fit residues: 86.7244 Evaluate side-chains 105 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 724 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN D 111 GLN D 132 GLN D 166 ASN B 95 GLN B 119 GLN B 156 GLN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067707 restraints weight = 17131.411| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.60 r_work: 0.2726 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9474 Z= 0.105 Angle : 0.513 7.019 12855 Z= 0.264 Chirality : 0.041 0.139 1485 Planarity : 0.004 0.041 1659 Dihedral : 4.867 40.229 1303 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.55 % Allowed : 8.71 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.62 (0.25), residues: 1175 helix: 0.98 (0.23), residues: 540 sheet: -0.03 (0.41), residues: 174 loop : 0.07 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 723 TYR 0.009 0.001 TYR C 260 PHE 0.012 0.001 PHE D 76 TRP 0.006 0.001 TRP C 639 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9473) covalent geometry : angle 0.51349 (12855) hydrogen bonds : bond 0.03773 ( 419) hydrogen bonds : angle 4.76105 ( 1164) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.444 Fit side-chains REVERT: D 132 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8691 (mm110) REVERT: B 52 LEU cc_start: 0.7066 (mm) cc_final: 0.6607 (mt) REVERT: B 138 ASN cc_start: 0.8990 (m-40) cc_final: 0.8578 (m-40) REVERT: B 153 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8412 (ttt-90) REVERT: A 140 ASP cc_start: 0.8707 (m-30) cc_final: 0.8310 (m-30) REVERT: A 180 ASN cc_start: 0.8989 (t0) cc_final: 0.8152 (t0) REVERT: C 188 THR cc_start: 0.9120 (m) cc_final: 0.8882 (t) REVERT: C 248 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8060 (ttp80) outliers start: 16 outliers final: 4 residues processed: 118 average time/residue: 0.5692 time to fit residues: 72.0335 Evaluate side-chains 100 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 254 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN B 156 GLN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.064975 restraints weight = 17276.698| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.61 r_work: 0.2675 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9474 Z= 0.187 Angle : 0.542 5.951 12855 Z= 0.278 Chirality : 0.043 0.177 1485 Planarity : 0.004 0.040 1659 Dihedral : 4.432 35.010 1293 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.23 % Allowed : 9.68 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.59 (0.25), residues: 1175 helix: 0.95 (0.23), residues: 539 sheet: -0.12 (0.41), residues: 176 loop : 0.11 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 534 TYR 0.010 0.001 TYR C 624 PHE 0.015 0.001 PHE A 84 TRP 0.008 0.001 TRP C 620 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9473) covalent geometry : angle 0.54222 (12855) hydrogen bonds : bond 0.03866 ( 419) hydrogen bonds : angle 4.62957 ( 1164) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.272 Fit side-chains REVERT: D 132 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8380 (mp10) REVERT: B 94 ASP cc_start: 0.8260 (p0) cc_final: 0.7876 (t0) REVERT: B 138 ASN cc_start: 0.9035 (m-40) cc_final: 0.8668 (m-40) REVERT: A 140 ASP cc_start: 0.8700 (m-30) cc_final: 0.8365 (m-30) REVERT: A 180 ASN cc_start: 0.9023 (t0) cc_final: 0.8145 (t0) REVERT: C 188 THR cc_start: 0.9154 (m) cc_final: 0.8946 (t) REVERT: C 248 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8090 (ttp80) REVERT: C 664 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8380 (mtp180) outliers start: 23 outliers final: 6 residues processed: 125 average time/residue: 0.5477 time to fit residues: 73.6776 Evaluate side-chains 105 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 664 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN B 156 GLN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.066697 restraints weight = 17278.979| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.61 r_work: 0.2706 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9474 Z= 0.109 Angle : 0.512 7.109 12855 Z= 0.262 Chirality : 0.042 0.173 1485 Planarity : 0.004 0.039 1659 Dihedral : 4.276 32.688 1293 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.65 % Allowed : 11.33 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.63 (0.25), residues: 1175 helix: 1.01 (0.23), residues: 540 sheet: -0.14 (0.42), residues: 176 loop : 0.13 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 534 TYR 0.007 0.001 TYR C 624 PHE 0.010 0.001 PHE A 84 TRP 0.008 0.001 TRP C 639 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9473) covalent geometry : angle 0.51185 (12855) hydrogen bonds : bond 0.03248 ( 419) hydrogen bonds : angle 4.53132 ( 1164) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.265 Fit side-chains REVERT: D 132 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8337 (mp10) REVERT: D 162 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7752 (mt-10) REVERT: B 94 ASP cc_start: 0.8223 (p0) cc_final: 0.7819 (t0) REVERT: B 138 ASN cc_start: 0.9013 (m-40) cc_final: 0.8651 (m-40) REVERT: A 140 ASP cc_start: 0.8717 (m-30) cc_final: 0.8297 (m-30) REVERT: A 180 ASN cc_start: 0.8960 (t0) cc_final: 0.8047 (t0) REVERT: C 188 THR cc_start: 0.9131 (m) cc_final: 0.8911 (t) REVERT: C 248 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8071 (ttp80) REVERT: C 397 MET cc_start: 0.9104 (mmm) cc_final: 0.8879 (mmp) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 0.5278 time to fit residues: 70.5785 Evaluate side-chains 112 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 254 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.067497 restraints weight = 17199.963| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.61 r_work: 0.2726 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 9474 Z= 0.103 Angle : 0.499 7.089 12855 Z= 0.255 Chirality : 0.041 0.166 1485 Planarity : 0.004 0.038 1659 Dihedral : 4.142 30.007 1293 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.65 % Allowed : 12.10 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1175 helix: 1.11 (0.23), residues: 540 sheet: -0.16 (0.42), residues: 176 loop : 0.16 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.007 0.001 TYR C 260 PHE 0.011 0.001 PHE D 76 TRP 0.008 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9473) covalent geometry : angle 0.49925 (12855) hydrogen bonds : bond 0.03040 ( 419) hydrogen bonds : angle 4.43206 ( 1164) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.424 Fit side-chains REVERT: D 132 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8329 (mp10) REVERT: D 162 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 94 ASP cc_start: 0.8171 (p0) cc_final: 0.7785 (t0) REVERT: B 100 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8541 (mm-30) REVERT: B 138 ASN cc_start: 0.9014 (m-40) cc_final: 0.8665 (m-40) REVERT: A 140 ASP cc_start: 0.8732 (m-30) cc_final: 0.8331 (m-30) REVERT: A 180 ASN cc_start: 0.8917 (t0) cc_final: 0.8005 (t0) REVERT: C 188 THR cc_start: 0.9098 (m) cc_final: 0.8881 (t) REVERT: C 248 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8101 (ttp80) REVERT: C 397 MET cc_start: 0.9132 (mmm) cc_final: 0.8908 (mmp) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.5740 time to fit residues: 74.7013 Evaluate side-chains 118 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.066322 restraints weight = 17195.671| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.61 r_work: 0.2705 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9474 Z= 0.132 Angle : 0.519 7.711 12855 Z= 0.263 Chirality : 0.042 0.166 1485 Planarity : 0.004 0.038 1659 Dihedral : 4.215 34.061 1293 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 12.49 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.75 (0.25), residues: 1175 helix: 1.16 (0.23), residues: 541 sheet: -0.19 (0.41), residues: 176 loop : 0.16 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.008 0.001 TYR C 624 PHE 0.012 0.001 PHE A 84 TRP 0.006 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9473) covalent geometry : angle 0.51892 (12855) hydrogen bonds : bond 0.03217 ( 419) hydrogen bonds : angle 4.40112 ( 1164) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.347 Fit side-chains REVERT: D 132 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8301 (mp10) REVERT: D 162 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 94 ASP cc_start: 0.8205 (p0) cc_final: 0.7838 (t0) REVERT: B 99 PHE cc_start: 0.8164 (m-80) cc_final: 0.7950 (m-80) REVERT: B 100 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8528 (mm-30) REVERT: B 138 ASN cc_start: 0.9018 (m-40) cc_final: 0.8667 (m-40) REVERT: B 153 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8164 (ttp-170) REVERT: A 140 ASP cc_start: 0.8724 (m-30) cc_final: 0.8343 (m-30) REVERT: A 180 ASN cc_start: 0.8915 (t0) cc_final: 0.8003 (t0) REVERT: C 248 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8119 (ttp80) REVERT: C 397 MET cc_start: 0.9158 (mmm) cc_final: 0.8939 (mmp) outliers start: 16 outliers final: 10 residues processed: 121 average time/residue: 0.5746 time to fit residues: 74.7104 Evaluate side-chains 121 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 0.0170 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.067070 restraints weight = 17265.461| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.63 r_work: 0.2721 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9474 Z= 0.108 Angle : 0.528 10.237 12855 Z= 0.264 Chirality : 0.041 0.163 1485 Planarity : 0.003 0.038 1659 Dihedral : 4.037 30.356 1291 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.74 % Allowed : 12.88 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1175 helix: 1.21 (0.23), residues: 542 sheet: -0.21 (0.41), residues: 176 loop : 0.18 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.011 0.001 TYR A 131 PHE 0.010 0.001 PHE A 84 TRP 0.007 0.001 TRP C 639 HIS 0.007 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9473) covalent geometry : angle 0.52842 (12855) hydrogen bonds : bond 0.03031 ( 419) hydrogen bonds : angle 4.38844 ( 1164) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.402 Fit side-chains REVERT: D 132 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8310 (mp10) REVERT: D 162 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 32 MET cc_start: 0.4748 (mmp) cc_final: 0.4315 (tmm) REVERT: B 50 LYS cc_start: 0.7982 (tppt) cc_final: 0.7716 (tttm) REVERT: B 94 ASP cc_start: 0.8197 (p0) cc_final: 0.7823 (t0) REVERT: B 99 PHE cc_start: 0.8162 (m-80) cc_final: 0.7919 (m-80) REVERT: B 100 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8504 (mm-30) REVERT: B 138 ASN cc_start: 0.9007 (m-40) cc_final: 0.8665 (m-40) REVERT: A 140 ASP cc_start: 0.8735 (m-30) cc_final: 0.8329 (m-30) REVERT: A 151 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8754 (mtmm) REVERT: A 180 ASN cc_start: 0.8898 (t0) cc_final: 0.7990 (t0) REVERT: C 89 PHE cc_start: 0.9148 (m-80) cc_final: 0.8712 (m-80) REVERT: C 248 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8137 (ttp80) REVERT: C 397 MET cc_start: 0.9175 (mmm) cc_final: 0.8951 (mmp) outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 0.6264 time to fit residues: 83.7469 Evaluate side-chains 118 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.066392 restraints weight = 17215.072| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.61 r_work: 0.2708 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9474 Z= 0.132 Angle : 0.540 10.858 12855 Z= 0.270 Chirality : 0.042 0.164 1485 Planarity : 0.004 0.038 1659 Dihedral : 4.002 27.787 1289 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.26 % Allowed : 13.55 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1175 helix: 1.20 (0.23), residues: 542 sheet: -0.20 (0.41), residues: 176 loop : 0.20 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.009 0.001 TYR B 58 PHE 0.012 0.001 PHE A 84 TRP 0.006 0.001 TRP C 639 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9473) covalent geometry : angle 0.53972 (12855) hydrogen bonds : bond 0.03158 ( 419) hydrogen bonds : angle 4.38567 ( 1164) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.404 Fit side-chains REVERT: D 101 MET cc_start: 0.8545 (mmm) cc_final: 0.7955 (mpp) REVERT: D 132 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8304 (mp10) REVERT: D 162 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 94 ASP cc_start: 0.8207 (p0) cc_final: 0.7840 (t0) REVERT: B 99 PHE cc_start: 0.8139 (m-80) cc_final: 0.7914 (m-80) REVERT: B 100 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8509 (mm-30) REVERT: B 128 LYS cc_start: 0.8684 (mttm) cc_final: 0.8313 (ptpp) REVERT: B 138 ASN cc_start: 0.8993 (m-40) cc_final: 0.8655 (m-40) REVERT: B 153 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8151 (ttp-170) REVERT: A 140 ASP cc_start: 0.8750 (m-30) cc_final: 0.8350 (m-30) REVERT: A 180 ASN cc_start: 0.8906 (t0) cc_final: 0.7982 (t0) REVERT: C 89 PHE cc_start: 0.9169 (m-80) cc_final: 0.8736 (m-80) REVERT: C 248 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8130 (ttp80) REVERT: C 397 MET cc_start: 0.9182 (mmm) cc_final: 0.8959 (mmp) REVERT: C 718 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8699 (mt-10) outliers start: 13 outliers final: 8 residues processed: 116 average time/residue: 0.6637 time to fit residues: 82.2405 Evaluate side-chains 118 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066904 restraints weight = 17055.206| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.59 r_work: 0.2716 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9474 Z= 0.119 Angle : 0.552 10.142 12855 Z= 0.273 Chirality : 0.042 0.165 1485 Planarity : 0.003 0.038 1659 Dihedral : 3.919 15.098 1288 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.36 % Allowed : 13.55 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.76 (0.25), residues: 1175 helix: 1.15 (0.23), residues: 542 sheet: -0.20 (0.42), residues: 176 loop : 0.19 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.014 0.001 TYR A 131 PHE 0.010 0.001 PHE A 84 TRP 0.006 0.001 TRP C 639 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9473) covalent geometry : angle 0.55208 (12855) hydrogen bonds : bond 0.03117 ( 419) hydrogen bonds : angle 4.39120 ( 1164) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.381 Fit side-chains REVERT: D 70 ARG cc_start: 0.8371 (mpp-170) cc_final: 0.8160 (mmt180) REVERT: D 101 MET cc_start: 0.8551 (mmm) cc_final: 0.7981 (mpp) REVERT: D 132 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8323 (mp10) REVERT: D 162 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 32 MET cc_start: 0.4830 (mmp) cc_final: 0.4325 (tmm) REVERT: B 50 LYS cc_start: 0.7847 (tppt) cc_final: 0.7596 (tttm) REVERT: B 94 ASP cc_start: 0.8200 (p0) cc_final: 0.7831 (t0) REVERT: B 99 PHE cc_start: 0.8187 (m-80) cc_final: 0.7965 (m-80) REVERT: B 100 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8512 (mm-30) REVERT: B 128 LYS cc_start: 0.8721 (mttm) cc_final: 0.8491 (ptpt) REVERT: B 138 ASN cc_start: 0.8984 (m-40) cc_final: 0.8663 (m-40) REVERT: B 153 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8127 (ttp-170) REVERT: A 34 LYS cc_start: 0.9196 (pttp) cc_final: 0.8907 (pttt) REVERT: A 140 ASP cc_start: 0.8757 (m-30) cc_final: 0.8342 (m-30) REVERT: A 151 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8779 (mtmm) REVERT: A 180 ASN cc_start: 0.8894 (t0) cc_final: 0.7956 (t0) REVERT: C 248 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8143 (ttp80) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.6891 time to fit residues: 85.8191 Evaluate side-chains 117 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 114 optimal weight: 0.0030 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.067724 restraints weight = 17143.573| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.62 r_work: 0.2736 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 9474 Z= 0.101 Angle : 0.535 9.984 12855 Z= 0.267 Chirality : 0.041 0.165 1485 Planarity : 0.003 0.038 1659 Dihedral : 3.832 16.442 1288 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.06 % Allowed : 13.84 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.83 (0.25), residues: 1175 helix: 1.21 (0.23), residues: 542 sheet: -0.12 (0.41), residues: 179 loop : 0.20 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.010 0.001 TYR A 201 PHE 0.009 0.001 PHE A 84 TRP 0.008 0.001 TRP C 639 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9473) covalent geometry : angle 0.53482 (12855) hydrogen bonds : bond 0.02952 ( 419) hydrogen bonds : angle 4.35533 ( 1164) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.389 Fit side-chains REVERT: D 101 MET cc_start: 0.8567 (mmm) cc_final: 0.8006 (mpp) REVERT: D 132 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8689 (mm110) REVERT: B 32 MET cc_start: 0.4856 (mmp) cc_final: 0.4352 (tmm) REVERT: B 50 LYS cc_start: 0.7840 (tppt) cc_final: 0.7568 (tttm) REVERT: B 94 ASP cc_start: 0.8228 (p0) cc_final: 0.7873 (t0) REVERT: B 99 PHE cc_start: 0.8148 (m-80) cc_final: 0.7946 (m-80) REVERT: B 100 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8545 (mm-30) REVERT: B 128 LYS cc_start: 0.8707 (mttm) cc_final: 0.8410 (ptpp) REVERT: B 138 ASN cc_start: 0.8973 (m-40) cc_final: 0.8640 (m-40) REVERT: A 34 LYS cc_start: 0.9194 (pttp) cc_final: 0.8889 (pttt) REVERT: A 140 ASP cc_start: 0.8750 (m-30) cc_final: 0.8314 (m-30) REVERT: A 180 ASN cc_start: 0.8857 (t0) cc_final: 0.7929 (t0) REVERT: A 231 ASN cc_start: 0.9177 (m-40) cc_final: 0.8733 (m-40) REVERT: C 87 ASP cc_start: 0.8528 (p0) cc_final: 0.7925 (p0) REVERT: C 248 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8172 (ttp80) REVERT: C 680 MET cc_start: 0.9384 (mmt) cc_final: 0.9122 (mmt) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.6668 time to fit residues: 83.7459 Evaluate side-chains 115 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 266 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066293 restraints weight = 17081.012| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.61 r_work: 0.2707 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9474 Z= 0.138 Angle : 0.560 9.456 12855 Z= 0.278 Chirality : 0.042 0.166 1485 Planarity : 0.004 0.037 1659 Dihedral : 3.891 14.308 1288 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.97 % Allowed : 14.42 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.83 (0.25), residues: 1175 helix: 1.20 (0.23), residues: 542 sheet: -0.11 (0.41), residues: 179 loop : 0.22 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.013 0.001 TYR A 131 PHE 0.012 0.001 PHE A 84 TRP 0.012 0.001 TRP C 68 HIS 0.009 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9473) covalent geometry : angle 0.56044 (12855) hydrogen bonds : bond 0.03175 ( 419) hydrogen bonds : angle 4.39725 ( 1164) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.17 seconds wall clock time: 70 minutes 58.94 seconds (4258.94 seconds total)