Starting phenix.real_space_refine on Sat Jun 7 03:14:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zen_60040/06_2025/8zen_60040_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zen_60040/06_2025/8zen_60040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zen_60040/06_2025/8zen_60040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zen_60040/06_2025/8zen_60040.map" model { file = "/net/cci-nas-00/data/ceres_data/8zen_60040/06_2025/8zen_60040_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zen_60040/06_2025/8zen_60040_trim.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 12 5.49 5 S 48 5.16 5 C 5244 2.51 5 N 1439 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1162 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2993 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 369} Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2993 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 369} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2207 SG CYS C 244 45.271 50.394 53.953 1.00 65.54 S ATOM 2668 SG CYS C 305 42.868 51.887 51.962 1.00 70.70 S ATOM 5200 SG CYS D 244 33.584 56.661 82.900 1.00 86.54 S ATOM 5661 SG CYS D 305 34.077 56.824 86.308 1.00 71.41 S Time building chain proxies: 5.49, per 1000 atoms: 0.65 Number of scatterers: 8388 At special positions: 0 Unit cell: (70.192, 103.576, 136.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 12 15.00 O 1643 8.00 N 1439 7.00 C 5244 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 973.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 191 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 305 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 244 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 191 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 244 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 305 " 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 47.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 69 through 84 removed outlier: 4.120A pdb=" N GLN B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 116 through 120 removed outlier: 4.117A pdb=" N GLN B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.503A pdb=" N MET B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.742A pdb=" N LYS B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 167 removed outlier: 3.909A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 192 through 211 Processing helix chain 'C' and resid 122 through 142 removed outlier: 3.802A pdb=" N LYS C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.517A pdb=" N TYR C 146 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.692A pdb=" N ILE C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 214 removed outlier: 3.730A pdb=" N ARG C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 removed outlier: 3.881A pdb=" N ASN C 263 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.984A pdb=" N LEU C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 428 through 444 Processing helix chain 'C' and resid 452 through 460 removed outlier: 3.794A pdb=" N SER C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 477 Processing helix chain 'C' and resid 486 through 490 Processing helix chain 'D' and resid 121 through 142 removed outlier: 3.569A pdb=" N GLU D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 150 removed outlier: 4.012A pdb=" N LYS D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.550A pdb=" N ILE D 180 " --> pdb=" O GLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 214 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 318 through 323 removed outlier: 4.103A pdb=" N LEU D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.685A pdb=" N LEU D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.569A pdb=" N SER D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 388 " --> pdb=" O ALA D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.727A pdb=" N MET D 491 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 84 removed outlier: 3.721A pdb=" N GLN E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.538A pdb=" N CYS E 101 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.686A pdb=" N ASN E 108 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.533A pdb=" N GLN E 119 " --> pdb=" O THR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.525A pdb=" N GLN E 131 " --> pdb=" O MET E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.530A pdb=" N PHE E 136 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 177 through 191 Processing helix chain 'E' and resid 192 through 211 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.744A pdb=" N VAL E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.615A pdb=" N VAL C 155 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA C 153 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER C 332 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE C 235 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 334 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 237 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL C 336 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 239 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.740A pdb=" N MET C 392 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 220 through 222 Processing sheet with id=AA4, first strand: chain 'C' and resid 278 through 279 Processing sheet with id=AA5, first strand: chain 'C' and resid 410 through 415 removed outlier: 3.608A pdb=" N ASP C 415 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 368 through 371 removed outlier: 3.729A pdb=" N GLY D 370 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 336 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER D 332 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE D 235 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 334 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 237 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL D 336 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 239 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 392 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 371 removed outlier: 3.729A pdb=" N GLY D 370 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 336 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER D 332 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE D 235 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 334 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 237 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL D 336 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 239 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 220 through 222 Processing sheet with id=AA9, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AB1, first strand: chain 'D' and resid 411 through 414 Processing sheet with id=AB2, first strand: chain 'D' and resid 446 through 447 removed outlier: 6.581A pdb=" N SER D 446 " --> pdb=" O ASN E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 374 hydrogen bonds defined for protein. 1020 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: 2.25 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2468 1.33 - 1.46: 1369 1.46 - 1.58: 4596 1.58 - 1.70: 9 1.70 - 1.82: 76 Bond restraints: 8518 Sorted by residual: bond pdb=" O16 IHP C 501 " pdb=" P6 IHP C 501 " ideal model delta sigma weight residual 1.672 1.565 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O12 IHP D 501 " pdb=" P2 IHP D 501 " ideal model delta sigma weight residual 1.675 1.568 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O14 IHP C 501 " pdb=" P4 IHP C 501 " ideal model delta sigma weight residual 1.671 1.575 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O15 IHP D 501 " pdb=" P5 IHP D 501 " ideal model delta sigma weight residual 1.675 1.589 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O12 IHP C 501 " pdb=" P2 IHP C 501 " ideal model delta sigma weight residual 1.675 1.591 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 8513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 11389 3.45 - 6.89: 104 6.89 - 10.34: 21 10.34 - 13.79: 5 13.79 - 17.24: 3 Bond angle restraints: 11522 Sorted by residual: angle pdb=" CB MET E 158 " pdb=" CG MET E 158 " pdb=" SD MET E 158 " ideal model delta sigma weight residual 112.70 129.94 -17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C1 IHP D 501 " pdb=" C2 IHP D 501 " pdb=" C3 IHP D 501 " ideal model delta sigma weight residual 108.51 123.79 -15.28 3.00e+00 1.11e-01 2.59e+01 angle pdb=" C2 IHP D 501 " pdb=" O12 IHP D 501 " pdb=" P2 IHP D 501 " ideal model delta sigma weight residual 123.98 108.89 15.09 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C4 IHP D 501 " pdb=" C5 IHP D 501 " pdb=" C6 IHP D 501 " ideal model delta sigma weight residual 109.60 121.71 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C1 IHP D 501 " pdb=" C6 IHP D 501 " pdb=" C5 IHP D 501 " ideal model delta sigma weight residual 108.26 119.67 -11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 11517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 5045 32.46 - 64.92: 208 64.92 - 97.38: 27 97.38 - 129.83: 8 129.83 - 162.29: 2 Dihedral angle restraints: 5290 sinusoidal: 2185 harmonic: 3105 Sorted by residual: dihedral pdb=" CA MET C 296 " pdb=" C MET C 296 " pdb=" N GLY C 297 " pdb=" CA GLY C 297 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C6 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C2 IHP C 501 " pdb=" O12 IHP C 501 " ideal model delta sinusoidal sigma weight residual 61.05 -136.66 -162.29 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C4 IHP C 501 " pdb=" C2 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " ideal model delta sinusoidal sigma weight residual 60.90 -137.89 -161.21 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.957: 1317 0.957 - 1.913: 0 1.913 - 2.870: 0 2.870 - 3.826: 0 3.826 - 4.783: 8 Chirality restraints: 1325 Sorted by residual: chirality pdb=" C2 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.52 2.26 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" C5 IHP C 501 " pdb=" C4 IHP C 501 " pdb=" C6 IHP C 501 " pdb=" O15 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.42 2.34 -4.76 2.00e-01 2.50e+01 5.66e+02 chirality pdb=" C2 IHP D 501 " pdb=" C1 IHP D 501 " pdb=" C3 IHP D 501 " pdb=" O12 IHP D 501 " both_signs ideal model delta sigma weight residual False -2.52 2.10 -4.62 2.00e-01 2.50e+01 5.34e+02 ... (remaining 1322 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 121 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C THR D 121 " 0.042 2.00e-02 2.50e+03 pdb=" O THR D 121 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 122 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 158 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C MET E 158 " -0.039 2.00e-02 2.50e+03 pdb=" O MET E 158 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP E 159 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 163 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ILE E 163 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE E 163 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL E 164 " -0.010 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 557 2.73 - 3.27: 9120 3.27 - 3.81: 14087 3.81 - 4.36: 17260 4.36 - 4.90: 29083 Nonbonded interactions: 70107 Sorted by model distance: nonbonded pdb=" OE1 GLU D 368 " pdb=" OG SER E 106 " model vdw 2.187 3.040 nonbonded pdb=" N GLN E 152 " pdb=" OE1 GLN E 152 " model vdw 2.209 3.120 nonbonded pdb=" OG SER D 304 " pdb=" OD2 ASP D 307 " model vdw 2.221 3.040 nonbonded pdb=" O GLN E 119 " pdb=" NE2 GLN E 121 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP D 189 " pdb=" NZ LYS D 270 " model vdw 2.253 3.120 ... (remaining 70102 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 217)) selection = (chain 'E' and resid 67 through 217) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.540 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.017 0.870 8528 Z= 1.508 Angle : 0.917 17.237 11522 Z= 0.449 Chirality : 0.361 4.783 1325 Planarity : 0.004 0.035 1473 Dihedral : 18.554 162.292 3272 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.76 % Allowed : 26.67 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1061 helix: 0.57 (0.26), residues: 393 sheet: 0.93 (0.45), residues: 122 loop : -0.12 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.007 0.001 HIS C 130 PHE 0.024 0.002 PHE D 124 TYR 0.029 0.001 TYR D 350 ARG 0.005 0.000 ARG D 386 Details of bonding type rmsd hydrogen bonds : bond 0.19390 ( 359) hydrogen bonds : angle 6.67705 ( 1020) metal coordination : bond 0.26258 ( 6) covalent geometry : bond 0.00655 ( 8518) covalent geometry : angle 0.91748 (11522) Misc. bond : bond 0.67215 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.942 Fit side-chains REVERT: B 135 LYS cc_start: 0.7582 (ptpp) cc_final: 0.7260 (ptmm) REVERT: B 168 LYS cc_start: 0.7747 (tppt) cc_final: 0.6843 (tptt) REVERT: B 209 LYS cc_start: 0.8128 (tppp) cc_final: 0.7544 (ttpt) REVERT: B 210 GLU cc_start: 0.6755 (tp30) cc_final: 0.6449 (tp30) REVERT: C 141 ASN cc_start: 0.7892 (m-40) cc_final: 0.7639 (m-40) REVERT: C 273 LYS cc_start: 0.7203 (tmtt) cc_final: 0.6868 (ptpt) REVERT: C 299 ARG cc_start: 0.6420 (mmm-85) cc_final: 0.6188 (mmm160) REVERT: C 346 ARG cc_start: 0.7377 (ttp80) cc_final: 0.7033 (ttp-110) REVERT: D 221 THR cc_start: 0.8058 (t) cc_final: 0.7662 (p) REVERT: D 222 LYS cc_start: 0.7956 (tttp) cc_final: 0.7683 (tptp) REVERT: D 273 LYS cc_start: 0.7234 (tppt) cc_final: 0.6409 (tmtt) REVERT: D 406 THR cc_start: 0.8585 (m) cc_final: 0.8286 (p) REVERT: D 491 MET cc_start: 0.7746 (mtp) cc_final: 0.7493 (mtm) REVERT: E 142 LYS cc_start: 0.6835 (pmtt) cc_final: 0.6426 (mppt) REVERT: E 152 GLN cc_start: 0.6617 (mp10) cc_final: 0.3839 (tm-30) REVERT: E 198 LYS cc_start: 0.7652 (mmpt) cc_final: 0.7157 (mtmt) REVERT: E 209 LYS cc_start: 0.7401 (tmmt) cc_final: 0.6835 (ttmm) outliers start: 16 outliers final: 7 residues processed: 176 average time/residue: 1.3802 time to fit residues: 257.0280 Evaluate side-chains 120 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 0.0030 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.0030 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 186 ASN C 461 GLN C 476 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.178594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133386 restraints weight = 9513.955| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.97 r_work: 0.3401 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8528 Z= 0.141 Angle : 0.731 12.493 11522 Z= 0.349 Chirality : 0.051 0.548 1325 Planarity : 0.004 0.035 1473 Dihedral : 7.626 58.147 1233 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.61 % Allowed : 23.82 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1061 helix: 0.77 (0.25), residues: 407 sheet: 0.91 (0.49), residues: 105 loop : -0.24 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 473 HIS 0.009 0.002 HIS C 130 PHE 0.017 0.002 PHE D 124 TYR 0.013 0.001 TYR D 205 ARG 0.005 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 359) hydrogen bonds : angle 4.84132 ( 1020) metal coordination : bond 0.01926 ( 6) covalent geometry : bond 0.00316 ( 8518) covalent geometry : angle 0.73114 (11522) Misc. bond : bond 0.00160 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: B 168 LYS cc_start: 0.7964 (tppt) cc_final: 0.7151 (tptt) REVERT: B 198 LYS cc_start: 0.8267 (mttt) cc_final: 0.7848 (mtmt) REVERT: B 201 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: B 209 LYS cc_start: 0.8167 (tppp) cc_final: 0.7344 (pttt) REVERT: C 136 TYR cc_start: 0.8013 (m-80) cc_final: 0.7744 (m-80) REVERT: C 150 LYS cc_start: 0.7617 (mmtp) cc_final: 0.7140 (mmpt) REVERT: C 266 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7561 (mtp85) REVERT: C 284 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6558 (pt0) REVERT: C 299 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6752 (mmm160) REVERT: C 346 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7195 (ttp-110) REVERT: C 347 LYS cc_start: 0.8249 (tppt) cc_final: 0.7935 (mptt) REVERT: C 371 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6698 (pm20) REVERT: C 462 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7969 (mp0) REVERT: D 263 ASN cc_start: 0.5817 (OUTLIER) cc_final: 0.5558 (t0) REVERT: D 338 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6331 (mt-10) REVERT: D 471 ILE cc_start: 0.8105 (mm) cc_final: 0.7839 (mm) REVERT: E 122 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: E 142 LYS cc_start: 0.6776 (pmtt) cc_final: 0.6457 (mppt) REVERT: E 152 GLN cc_start: 0.6806 (mp10) cc_final: 0.6531 (mp10) REVERT: E 198 LYS cc_start: 0.7720 (mmpt) cc_final: 0.7345 (mtmt) REVERT: E 201 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: E 209 LYS cc_start: 0.7598 (tmmt) cc_final: 0.7044 (ttmm) outliers start: 42 outliers final: 13 residues processed: 148 average time/residue: 1.2636 time to fit residues: 198.6183 Evaluate side-chains 127 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 ASN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 ASN E 131 GLN E 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131025 restraints weight = 9697.383| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.75 r_work: 0.3374 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8528 Z= 0.141 Angle : 0.655 11.638 11522 Z= 0.325 Chirality : 0.047 0.400 1325 Planarity : 0.004 0.036 1473 Dihedral : 7.672 54.236 1227 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.50 % Allowed : 23.16 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1061 helix: 0.74 (0.25), residues: 409 sheet: 1.84 (0.53), residues: 87 loop : -0.20 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 473 HIS 0.010 0.001 HIS C 130 PHE 0.014 0.001 PHE D 124 TYR 0.011 0.001 TYR D 205 ARG 0.006 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 359) hydrogen bonds : angle 4.57314 ( 1020) metal coordination : bond 0.00175 ( 6) covalent geometry : bond 0.00322 ( 8518) covalent geometry : angle 0.65509 (11522) Misc. bond : bond 0.00020 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 76 GLN cc_start: 0.7743 (mt0) cc_final: 0.7428 (mp10) REVERT: B 112 ASN cc_start: 0.6877 (OUTLIER) cc_final: 0.6496 (t0) REVERT: B 168 LYS cc_start: 0.8075 (tppt) cc_final: 0.7152 (tptt) REVERT: B 198 LYS cc_start: 0.8188 (mttt) cc_final: 0.7761 (mtmt) REVERT: B 201 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6683 (mt0) REVERT: B 209 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7439 (pttt) REVERT: C 150 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7214 (mmpt) REVERT: C 266 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7701 (mtp85) REVERT: C 284 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6596 (pt0) REVERT: C 299 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6964 (mmm160) REVERT: C 346 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7096 (ttm-80) REVERT: C 347 LYS cc_start: 0.8278 (tppt) cc_final: 0.7981 (mptt) REVERT: C 462 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7981 (mp0) REVERT: C 493 THR cc_start: 0.9254 (t) cc_final: 0.8965 (m) REVERT: D 176 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6995 (mtp85) REVERT: D 263 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5634 (t0) REVERT: D 405 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7612 (ttm170) REVERT: D 471 ILE cc_start: 0.8190 (mm) cc_final: 0.7925 (mm) REVERT: E 122 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: E 127 MET cc_start: 0.8224 (tmt) cc_final: 0.7916 (tmm) REVERT: E 142 LYS cc_start: 0.6769 (pmtt) cc_final: 0.6414 (mppt) REVERT: E 152 GLN cc_start: 0.6725 (mp10) cc_final: 0.3893 (tm-30) REVERT: E 198 LYS cc_start: 0.7780 (mmpt) cc_final: 0.7419 (mtpt) REVERT: E 201 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: E 209 LYS cc_start: 0.7640 (tmmt) cc_final: 0.7140 (ttmm) outliers start: 41 outliers final: 15 residues processed: 144 average time/residue: 1.3376 time to fit residues: 204.1914 Evaluate side-chains 131 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 0.0040 chunk 77 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133396 restraints weight = 9673.677| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.73 r_work: 0.3406 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8528 Z= 0.109 Angle : 0.590 10.609 11522 Z= 0.293 Chirality : 0.044 0.342 1325 Planarity : 0.003 0.036 1473 Dihedral : 7.354 56.127 1227 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.39 % Allowed : 23.16 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1061 helix: 0.90 (0.25), residues: 414 sheet: 1.76 (0.54), residues: 87 loop : -0.21 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 473 HIS 0.011 0.001 HIS C 130 PHE 0.013 0.001 PHE D 124 TYR 0.009 0.001 TYR D 205 ARG 0.005 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 359) hydrogen bonds : angle 4.31785 ( 1020) metal coordination : bond 0.00106 ( 6) covalent geometry : bond 0.00247 ( 8518) covalent geometry : angle 0.59025 (11522) Misc. bond : bond 0.00022 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.6884 (OUTLIER) cc_final: 0.6496 (t0) REVERT: B 168 LYS cc_start: 0.8090 (tppt) cc_final: 0.7199 (tptt) REVERT: B 198 LYS cc_start: 0.8115 (mttt) cc_final: 0.7672 (mtmt) REVERT: B 201 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6661 (mt0) REVERT: B 209 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7453 (pttt) REVERT: C 265 SER cc_start: 0.8918 (m) cc_final: 0.8632 (p) REVERT: C 266 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7785 (mtp85) REVERT: C 299 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.7123 (mmm160) REVERT: C 347 LYS cc_start: 0.8285 (tppt) cc_final: 0.7997 (mptt) REVERT: C 368 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: C 392 MET cc_start: 0.8549 (ppp) cc_final: 0.8280 (ppp) REVERT: C 410 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7260 (mmt) REVERT: C 493 THR cc_start: 0.9300 (t) cc_final: 0.9039 (m) REVERT: D 176 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7000 (mtp85) REVERT: D 263 ASN cc_start: 0.5943 (OUTLIER) cc_final: 0.5666 (t0) REVERT: D 275 MET cc_start: 0.8102 (ptp) cc_final: 0.7845 (ptp) REVERT: D 405 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7620 (ttm170) REVERT: D 471 ILE cc_start: 0.8257 (mm) cc_final: 0.8002 (mm) REVERT: D 494 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6242 (pp) REVERT: E 122 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: E 198 LYS cc_start: 0.7820 (mmpt) cc_final: 0.7511 (mtpt) REVERT: E 201 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: E 209 LYS cc_start: 0.7643 (tmmt) cc_final: 0.7128 (ttmm) outliers start: 40 outliers final: 15 residues processed: 148 average time/residue: 1.3166 time to fit residues: 206.7283 Evaluate side-chains 128 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 197 GLN B 201 GLN C 240 ASN C 341 ASN C 379 GLN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125766 restraints weight = 9582.490| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.71 r_work: 0.3308 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8528 Z= 0.213 Angle : 0.675 12.612 11522 Z= 0.333 Chirality : 0.050 0.577 1325 Planarity : 0.004 0.048 1473 Dihedral : 7.460 55.412 1227 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.27 % Allowed : 22.61 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1061 helix: 0.57 (0.25), residues: 414 sheet: 1.56 (0.51), residues: 93 loop : -0.31 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 482 HIS 0.013 0.002 HIS C 130 PHE 0.014 0.002 PHE D 135 TYR 0.016 0.002 TYR C 453 ARG 0.003 0.000 ARG D 248 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 359) hydrogen bonds : angle 4.60936 ( 1020) metal coordination : bond 0.00515 ( 6) covalent geometry : bond 0.00520 ( 8518) covalent geometry : angle 0.67522 (11522) Misc. bond : bond 0.00073 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 76 GLN cc_start: 0.7860 (mt0) cc_final: 0.7558 (mp10) REVERT: B 112 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6618 (t0) REVERT: B 135 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7747 (mtmm) REVERT: B 168 LYS cc_start: 0.8310 (tppt) cc_final: 0.7311 (tptt) REVERT: B 198 LYS cc_start: 0.8290 (mttt) cc_final: 0.7951 (mppt) REVERT: B 209 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7689 (ttpt) REVERT: C 150 LYS cc_start: 0.7766 (mmtm) cc_final: 0.7480 (mmpt) REVERT: C 266 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7848 (mtp85) REVERT: C 299 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7202 (mmm160) REVERT: C 347 LYS cc_start: 0.8434 (tppt) cc_final: 0.8135 (mptt) REVERT: C 371 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: C 405 ARG cc_start: 0.7689 (tpp80) cc_final: 0.7269 (ttm110) REVERT: C 410 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7297 (mmt) REVERT: C 462 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8108 (mp0) REVERT: C 493 THR cc_start: 0.9325 (t) cc_final: 0.9102 (m) REVERT: D 176 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6995 (mtp85) REVERT: D 263 ASN cc_start: 0.6087 (OUTLIER) cc_final: 0.5702 (t0) REVERT: D 275 MET cc_start: 0.8349 (ptp) cc_final: 0.8104 (ptp) REVERT: D 371 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6296 (mm-30) REVERT: D 405 ARG cc_start: 0.8310 (ttm170) cc_final: 0.7838 (ttm170) REVERT: D 494 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6809 (pp) REVERT: E 78 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6420 (mp) REVERT: E 122 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: E 137 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7314 (mtmm) REVERT: E 142 LYS cc_start: 0.6601 (pmtt) cc_final: 0.6348 (mppt) REVERT: E 198 LYS cc_start: 0.7856 (mmpt) cc_final: 0.7567 (mtpt) REVERT: E 201 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: E 209 LYS cc_start: 0.7737 (tmmt) cc_final: 0.7190 (ttmm) outliers start: 48 outliers final: 21 residues processed: 146 average time/residue: 1.2937 time to fit residues: 200.2335 Evaluate side-chains 143 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.175814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128793 restraints weight = 9547.210| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.72 r_work: 0.3345 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.131 Angle : 0.604 9.333 11522 Z= 0.301 Chirality : 0.045 0.358 1325 Planarity : 0.004 0.038 1473 Dihedral : 7.163 57.308 1227 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.28 % Allowed : 24.48 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1061 helix: 0.72 (0.25), residues: 414 sheet: 1.55 (0.52), residues: 93 loop : -0.25 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.012 0.001 HIS C 130 PHE 0.011 0.001 PHE D 124 TYR 0.008 0.001 TYR D 205 ARG 0.002 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 359) hydrogen bonds : angle 4.41288 ( 1020) metal coordination : bond 0.00213 ( 6) covalent geometry : bond 0.00309 ( 8518) covalent geometry : angle 0.60386 (11522) Misc. bond : bond 0.00028 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.024 Fit side-chains REVERT: B 76 GLN cc_start: 0.7837 (mt0) cc_final: 0.7602 (mp10) REVERT: B 112 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6677 (t0) REVERT: B 135 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7764 (mtmm) REVERT: B 168 LYS cc_start: 0.8269 (tppt) cc_final: 0.7246 (tptt) REVERT: B 209 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7683 (ttpt) REVERT: B 210 GLU cc_start: 0.6934 (tp30) cc_final: 0.6650 (tp30) REVERT: C 150 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7265 (mmpt) REVERT: C 266 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7824 (mtp-110) REVERT: C 299 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7248 (mmp-170) REVERT: C 347 LYS cc_start: 0.8389 (tppt) cc_final: 0.8100 (mptt) REVERT: C 410 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7267 (mmt) REVERT: C 493 THR cc_start: 0.9310 (t) cc_final: 0.9071 (m) REVERT: D 176 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6989 (mtp85) REVERT: D 263 ASN cc_start: 0.6001 (OUTLIER) cc_final: 0.5678 (t0) REVERT: D 275 MET cc_start: 0.8347 (ptp) cc_final: 0.8112 (ptp) REVERT: D 346 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6598 (mmm160) REVERT: D 405 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7907 (ttm170) REVERT: D 494 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6942 (pp) REVERT: E 78 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6654 (mt) REVERT: E 122 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: E 137 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7317 (mtmm) REVERT: E 142 LYS cc_start: 0.6525 (pmtt) cc_final: 0.6284 (mppt) REVERT: E 198 LYS cc_start: 0.7814 (mmpt) cc_final: 0.7530 (mtpt) REVERT: E 201 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: E 209 LYS cc_start: 0.7727 (tmmt) cc_final: 0.7197 (ttmm) outliers start: 39 outliers final: 17 residues processed: 144 average time/residue: 1.3741 time to fit residues: 210.1543 Evaluate side-chains 138 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 461 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.176653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129613 restraints weight = 9616.341| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.73 r_work: 0.3354 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.123 Angle : 0.598 8.359 11522 Z= 0.297 Chirality : 0.045 0.330 1325 Planarity : 0.004 0.037 1473 Dihedral : 6.962 59.463 1226 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.28 % Allowed : 23.93 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1061 helix: 0.78 (0.25), residues: 414 sheet: 1.34 (0.53), residues: 96 loop : -0.17 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.012 0.001 HIS C 130 PHE 0.023 0.001 PHE B 177 TYR 0.008 0.001 TYR D 205 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 359) hydrogen bonds : angle 4.34076 ( 1020) metal coordination : bond 0.00180 ( 6) covalent geometry : bond 0.00288 ( 8518) covalent geometry : angle 0.59830 (11522) Misc. bond : bond 0.00022 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.003 Fit side-chains REVERT: B 76 GLN cc_start: 0.7874 (mt0) cc_final: 0.7624 (mp10) REVERT: B 112 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.6626 (t0) REVERT: B 135 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7767 (mtmm) REVERT: B 168 LYS cc_start: 0.8293 (tppt) cc_final: 0.7250 (tptt) REVERT: B 201 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7273 (mm-40) REVERT: B 209 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7660 (ttpt) REVERT: B 210 GLU cc_start: 0.7002 (tp30) cc_final: 0.6755 (tp30) REVERT: C 150 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7223 (mmpt) REVERT: C 266 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7818 (mtp-110) REVERT: C 299 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7332 (mtp180) REVERT: C 347 LYS cc_start: 0.8389 (tppt) cc_final: 0.8088 (mptt) REVERT: C 368 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: C 392 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8305 (ppp) REVERT: C 410 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7243 (mmt) REVERT: C 493 THR cc_start: 0.9297 (t) cc_final: 0.9045 (m) REVERT: D 176 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7033 (mtp85) REVERT: D 263 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.5628 (t0) REVERT: D 275 MET cc_start: 0.8340 (ptp) cc_final: 0.8138 (ptp) REVERT: D 371 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6068 (mm-30) REVERT: D 405 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7870 (ttm170) REVERT: D 494 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.7005 (pp) REVERT: E 78 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6465 (mt) REVERT: E 122 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: E 137 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7312 (mtmm) REVERT: E 142 LYS cc_start: 0.6380 (pmtt) cc_final: 0.6157 (mppt) REVERT: E 174 SER cc_start: 0.4991 (p) cc_final: 0.4747 (m) REVERT: E 198 LYS cc_start: 0.7872 (mmpt) cc_final: 0.7568 (mtpt) REVERT: E 201 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: E 209 LYS cc_start: 0.7616 (tmmt) cc_final: 0.7184 (ttmm) outliers start: 39 outliers final: 18 residues processed: 142 average time/residue: 1.3324 time to fit residues: 201.1393 Evaluate side-chains 145 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 240 ASN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 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 = 0.4043 r_free = 0.4043 target = 0.174764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128073 restraints weight = 9691.146| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.69 r_work: 0.3346 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.142 Angle : 0.618 9.529 11522 Z= 0.307 Chirality : 0.046 0.378 1325 Planarity : 0.004 0.035 1473 Dihedral : 6.950 59.362 1226 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.28 % Allowed : 24.15 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1061 helix: 0.75 (0.25), residues: 414 sheet: 1.45 (0.53), residues: 95 loop : -0.25 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.012 0.001 HIS C 130 PHE 0.019 0.002 PHE B 177 TYR 0.008 0.001 TYR D 205 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 359) hydrogen bonds : angle 4.35059 ( 1020) metal coordination : bond 0.00262 ( 6) covalent geometry : bond 0.00340 ( 8518) covalent geometry : angle 0.61779 (11522) Misc. bond : bond 0.00033 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.022 Fit side-chains REVERT: B 76 GLN cc_start: 0.7938 (mt0) cc_final: 0.7729 (mp10) REVERT: B 112 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.6689 (t0) REVERT: B 135 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7794 (mtmm) REVERT: B 168 LYS cc_start: 0.8374 (tppt) cc_final: 0.7287 (tptt) REVERT: B 201 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7291 (mt0) REVERT: B 209 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7641 (ttpt) REVERT: B 210 GLU cc_start: 0.6966 (tp30) cc_final: 0.6724 (tp30) REVERT: C 150 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7226 (mmpt) REVERT: C 266 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7826 (mtp-110) REVERT: C 299 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7365 (mtp180) REVERT: C 347 LYS cc_start: 0.8401 (tppt) cc_final: 0.8105 (mptt) REVERT: C 392 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8291 (ppp) REVERT: C 410 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7263 (mmt) REVERT: C 462 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8161 (mp0) REVERT: C 493 THR cc_start: 0.9306 (t) cc_final: 0.9051 (m) REVERT: D 263 ASN cc_start: 0.5866 (OUTLIER) cc_final: 0.5598 (t0) REVERT: D 275 MET cc_start: 0.8339 (ptp) cc_final: 0.8131 (ptp) REVERT: D 405 ARG cc_start: 0.8278 (ttm170) cc_final: 0.7962 (ttm170) REVERT: D 494 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7152 (pp) REVERT: E 78 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6523 (mt) REVERT: E 122 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: E 137 LYS cc_start: 0.8105 (mmtp) cc_final: 0.7445 (mtmm) REVERT: E 142 LYS cc_start: 0.6350 (pmtt) cc_final: 0.6140 (mppt) REVERT: E 158 MET cc_start: 0.5939 (mpp) cc_final: 0.5176 (tpt) REVERT: E 174 SER cc_start: 0.5125 (p) cc_final: 0.4886 (m) REVERT: E 191 CYS cc_start: 0.6983 (m) cc_final: 0.6514 (m) REVERT: E 198 LYS cc_start: 0.7876 (mmpt) cc_final: 0.7569 (mtpt) REVERT: E 201 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: E 209 LYS cc_start: 0.7599 (tmmt) cc_final: 0.7206 (ttmm) outliers start: 39 outliers final: 21 residues processed: 142 average time/residue: 1.4235 time to fit residues: 214.4331 Evaluate side-chains 147 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127844 restraints weight = 9696.974| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.68 r_work: 0.3346 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8528 Z= 0.148 Angle : 0.625 9.636 11522 Z= 0.311 Chirality : 0.046 0.382 1325 Planarity : 0.004 0.037 1473 Dihedral : 6.945 59.267 1226 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.28 % Allowed : 24.48 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1061 helix: 0.72 (0.25), residues: 414 sheet: 1.35 (0.53), residues: 96 loop : -0.24 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.012 0.001 HIS C 130 PHE 0.024 0.002 PHE B 177 TYR 0.008 0.001 TYR D 205 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 359) hydrogen bonds : angle 4.38099 ( 1020) metal coordination : bond 0.00274 ( 6) covalent geometry : bond 0.00356 ( 8518) covalent geometry : angle 0.62471 (11522) Misc. bond : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.6676 (t0) REVERT: B 168 LYS cc_start: 0.8358 (tppt) cc_final: 0.7269 (tptt) REVERT: B 198 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7745 (mppt) REVERT: B 201 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: B 209 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7660 (ttpt) REVERT: C 150 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7244 (mmpt) REVERT: C 266 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7822 (mtp85) REVERT: C 299 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7358 (mtp180) REVERT: C 347 LYS cc_start: 0.8403 (tppt) cc_final: 0.8115 (mptt) REVERT: C 392 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8299 (ppp) REVERT: C 410 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7278 (mmt) REVERT: C 493 THR cc_start: 0.9304 (t) cc_final: 0.9038 (m) REVERT: D 176 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6764 (mtp85) REVERT: D 263 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.5608 (t0) REVERT: D 405 ARG cc_start: 0.8282 (ttm170) cc_final: 0.7963 (ttm170) REVERT: E 78 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6429 (mt) REVERT: E 122 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: E 137 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7483 (mtmm) REVERT: E 142 LYS cc_start: 0.6365 (pmtt) cc_final: 0.6135 (mppt) REVERT: E 158 MET cc_start: 0.5906 (mpp) cc_final: 0.5120 (tpt) REVERT: E 174 SER cc_start: 0.5056 (p) cc_final: 0.4823 (m) REVERT: E 191 CYS cc_start: 0.6996 (m) cc_final: 0.6532 (m) REVERT: E 198 LYS cc_start: 0.7835 (mmpt) cc_final: 0.7506 (mtpt) REVERT: E 201 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: E 209 LYS cc_start: 0.7677 (tmmt) cc_final: 0.7196 (ttmm) outliers start: 39 outliers final: 21 residues processed: 138 average time/residue: 1.4266 time to fit residues: 209.5103 Evaluate side-chains 141 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.177302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131288 restraints weight = 9594.937| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.66 r_work: 0.3392 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.113 Angle : 0.591 7.838 11522 Z= 0.297 Chirality : 0.044 0.290 1325 Planarity : 0.004 0.038 1473 Dihedral : 6.819 59.975 1226 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.51 % Allowed : 25.36 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1061 helix: 0.94 (0.25), residues: 414 sheet: 1.37 (0.53), residues: 96 loop : -0.18 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 482 HIS 0.010 0.001 HIS C 130 PHE 0.023 0.001 PHE B 177 TYR 0.008 0.001 TYR D 205 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 359) hydrogen bonds : angle 4.23083 ( 1020) metal coordination : bond 0.00131 ( 6) covalent geometry : bond 0.00261 ( 8518) covalent geometry : angle 0.59084 (11522) Misc. bond : bond 0.00013 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.6644 (t0) REVERT: B 168 LYS cc_start: 0.8408 (tppt) cc_final: 0.7292 (tptt) REVERT: B 198 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7749 (mppt) REVERT: B 209 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7633 (ttpt) REVERT: C 150 LYS cc_start: 0.7551 (mmtm) cc_final: 0.7190 (mmpt) REVERT: C 266 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7802 (mtp85) REVERT: C 275 MET cc_start: 0.6703 (tpt) cc_final: 0.6372 (tpt) REVERT: C 299 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7353 (mtp180) REVERT: C 347 LYS cc_start: 0.8398 (tppt) cc_final: 0.8109 (mptt) REVERT: C 368 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: C 410 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7247 (mmt) REVERT: C 493 THR cc_start: 0.9282 (t) cc_final: 0.9006 (m) REVERT: D 263 ASN cc_start: 0.5801 (OUTLIER) cc_final: 0.5584 (t0) REVERT: D 405 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7932 (ttm170) REVERT: E 142 LYS cc_start: 0.6223 (pmtt) cc_final: 0.5986 (mppt) REVERT: E 158 MET cc_start: 0.5586 (mpp) cc_final: 0.4968 (tpt) REVERT: E 174 SER cc_start: 0.5164 (p) cc_final: 0.4939 (m) REVERT: E 191 CYS cc_start: 0.6964 (m) cc_final: 0.6530 (m) REVERT: E 198 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7543 (mtpt) REVERT: E 201 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: E 209 LYS cc_start: 0.7602 (tmmt) cc_final: 0.7193 (ttmm) outliers start: 32 outliers final: 19 residues processed: 141 average time/residue: 1.3191 time to fit residues: 198.6858 Evaluate side-chains 133 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129995 restraints weight = 9729.076| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.68 r_work: 0.3371 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.130 Angle : 0.614 8.235 11522 Z= 0.307 Chirality : 0.045 0.337 1325 Planarity : 0.004 0.036 1473 Dihedral : 6.809 59.942 1226 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.29 % Allowed : 25.03 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1061 helix: 0.94 (0.25), residues: 415 sheet: 1.42 (0.53), residues: 96 loop : -0.19 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.011 0.001 HIS C 130 PHE 0.023 0.001 PHE B 177 TYR 0.007 0.001 TYR D 205 ARG 0.004 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 359) hydrogen bonds : angle 4.26494 ( 1020) metal coordination : bond 0.00210 ( 6) covalent geometry : bond 0.00308 ( 8518) covalent geometry : angle 0.61409 (11522) Misc. bond : bond 0.00026 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6234.08 seconds wall clock time: 108 minutes 40.36 seconds (6520.36 seconds total)