Starting phenix.real_space_refine on Wed Feb 4 01:53:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kv8_62588/02_2026/9kv8_62588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kv8_62588/02_2026/9kv8_62588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kv8_62588/02_2026/9kv8_62588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kv8_62588/02_2026/9kv8_62588.map" model { file = "/net/cci-nas-00/data/ceres_data/9kv8_62588/02_2026/9kv8_62588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kv8_62588/02_2026/9kv8_62588.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5242 2.51 5 N 1411 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8201 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2172 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1551 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2380 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 126 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 364 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1639 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 2.19, per 1000 atoms: 0.27 Number of scatterers: 8201 At special positions: 0 Unit cell: (86.698, 119.048, 121.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1496 8.00 N 1411 7.00 C 5242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 356.1 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 20 through 49 Processing helix chain 'C' and resid 57 through 84 removed outlier: 4.151A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 92 through 126 Proline residue: C 99 - end of helix Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 160 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 323 through 338 removed outlier: 3.758A pdb=" N MET C 327 " --> pdb=" O PRO C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 358 Processing helix chain 'C' and resid 364 through 396 Proline residue: C 385 - end of helix removed outlier: 4.121A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 429 removed outlier: 4.724A pdb=" N HIS C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N MET C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) Proline residue: C 425 - end of helix Processing helix chain 'C' and resid 432 through 443 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.761A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.578A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.620A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 218 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.053A pdb=" N LEU A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.804A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.046A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.594A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.646A pdb=" N LEU A 38 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.697A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.345A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.664A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.228A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.965A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.373A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.599A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.549A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.557A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 155 through 159 removed outlier: 3.610A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.585A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2664 1.34 - 1.46: 1780 1.46 - 1.57: 3875 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8387 Sorted by residual: bond pdb=" CA ASP B 247 " pdb=" C ASP B 247 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.80e-02 3.09e+03 1.53e+00 bond pdb=" CA VAL C 155 " pdb=" C VAL C 155 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.41e+00 bond pdb=" CB PHE C 176 " pdb=" CG PHE C 176 " ideal model delta sigma weight residual 1.502 1.480 0.022 2.30e-02 1.89e+03 8.77e-01 bond pdb=" CB VAL B 90 " pdb=" CG1 VAL B 90 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.33e-01 bond pdb=" CA GLY B 144 " pdb=" C GLY B 144 " ideal model delta sigma weight residual 1.519 1.511 0.007 8.90e-03 1.26e+04 7.07e-01 ... (remaining 8382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 11087 1.17 - 2.34: 279 2.34 - 3.51: 61 3.51 - 4.68: 18 4.68 - 5.85: 5 Bond angle restraints: 11450 Sorted by residual: angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.53 109.33 4.20 9.80e-01 1.04e+00 1.83e+01 angle pdb=" N SER C 364 " pdb=" CA SER C 364 " pdb=" C SER C 364 " ideal model delta sigma weight residual 114.56 110.96 3.60 1.27e+00 6.20e-01 8.06e+00 angle pdb=" N ASN C 175 " pdb=" CA ASN C 175 " pdb=" CB ASN C 175 " ideal model delta sigma weight residual 109.88 113.76 -3.88 1.58e+00 4.01e-01 6.04e+00 angle pdb=" CA VAL H 64 " pdb=" C VAL H 64 " pdb=" N LYS H 65 " ideal model delta sigma weight residual 119.31 116.51 2.80 1.15e+00 7.56e-01 5.93e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.47 126.85 -3.38 1.53e+00 4.27e-01 4.89e+00 ... (remaining 11445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4481 16.79 - 33.59: 322 33.59 - 50.38: 46 50.38 - 67.17: 6 67.17 - 83.96: 4 Dihedral angle restraints: 4859 sinusoidal: 1600 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 172 " pdb=" CB CYS C 172 " ideal model delta sinusoidal sigma weight residual -86.00 -163.30 77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CA TYR C 174 " pdb=" C TYR C 174 " pdb=" N ASN C 175 " pdb=" CA ASN C 175 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU C 84 " pdb=" C LEU C 84 " pdb=" N GLN C 85 " pdb=" CA GLN C 85 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 802 0.028 - 0.056: 327 0.056 - 0.084: 123 0.084 - 0.112: 69 0.112 - 0.140: 23 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CB THR C 359 " pdb=" CA THR C 359 " pdb=" OG1 THR C 359 " pdb=" CG2 THR C 359 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1341 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO G 49 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 175 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" CG ASN C 175 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 175 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 175 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 322 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO C 323 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 323 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 323 " -0.019 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1061 2.75 - 3.29: 8158 3.29 - 3.83: 13891 3.83 - 4.36: 15840 4.36 - 4.90: 28555 Nonbonded interactions: 67505 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.233 3.040 nonbonded pdb=" O CYS A 215 " pdb=" NE2 GLN B 75 " model vdw 2.234 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.234 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.242 3.040 ... (remaining 67500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.003 0.041 8390 Z= 0.133 Angle : 0.491 5.851 11456 Z= 0.273 Chirality : 0.041 0.140 1344 Planarity : 0.003 0.039 1459 Dihedral : 11.872 83.964 2742 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 1106 helix: 2.15 (0.26), residues: 397 sheet: -0.42 (0.33), residues: 252 loop : -0.25 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 98 TYR 0.012 0.001 TYR H 190 PHE 0.011 0.001 PHE H 68 TRP 0.006 0.001 TRP B 211 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8387) covalent geometry : angle 0.49054 (11450) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.72584 ( 6) hydrogen bonds : bond 0.17457 ( 451) hydrogen bonds : angle 7.26399 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6630 (mmp) cc_final: 0.6301 (mmm) REVERT: C 72 CYS cc_start: 0.7238 (m) cc_final: 0.6472 (m) REVERT: A 24 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7522 (mtmt) REVERT: A 213 ILE cc_start: 0.8027 (tp) cc_final: 0.7765 (tp) REVERT: A 252 ASP cc_start: 0.7563 (t0) cc_final: 0.7135 (t0) REVERT: A 253 SER cc_start: 0.8811 (t) cc_final: 0.8605 (t) REVERT: A 277 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7083 (mt-10) REVERT: A 336 PHE cc_start: 0.8257 (t80) cc_final: 0.7715 (t80) REVERT: A 353 LEU cc_start: 0.7115 (tp) cc_final: 0.6802 (tt) REVERT: B 32 GLN cc_start: 0.6813 (mt0) cc_final: 0.6537 (mt0) REVERT: B 49 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7854 (mmt180) REVERT: B 150 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7623 (mmt180) REVERT: B 301 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7898 (mtpp) REVERT: H 18 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7216 (ttm-80) REVERT: H 138 ILE cc_start: 0.8341 (mp) cc_final: 0.8078 (mt) REVERT: H 176 TRP cc_start: 0.8302 (m100) cc_final: 0.8005 (m100) REVERT: H 219 LEU cc_start: 0.7728 (tp) cc_final: 0.7406 (tp) REVERT: H 237 LEU cc_start: 0.8389 (mt) cc_final: 0.8159 (mp) REVERT: H 238 THR cc_start: 0.8108 (m) cc_final: 0.7829 (p) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1182 time to fit residues: 37.2672 Evaluate side-chains 211 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN B 340 ASN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115234 restraints weight = 12997.868| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.12 r_work: 0.3397 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8390 Z= 0.167 Angle : 0.539 6.716 11456 Z= 0.292 Chirality : 0.043 0.168 1344 Planarity : 0.004 0.042 1459 Dihedral : 4.111 21.624 1194 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.03 % Allowed : 10.14 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 1106 helix: 2.13 (0.27), residues: 399 sheet: -0.40 (0.33), residues: 248 loop : -0.33 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 129 TYR 0.019 0.002 TYR H 190 PHE 0.022 0.001 PHE C 176 TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8387) covalent geometry : angle 0.53848 (11450) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.57286 ( 6) hydrogen bonds : bond 0.04051 ( 451) hydrogen bonds : angle 5.57159 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.7017 (mmp) cc_final: 0.6550 (mmm) REVERT: C 160 TYR cc_start: 0.7086 (m-80) cc_final: 0.6845 (m-80) REVERT: C 423 PHE cc_start: 0.7926 (m-10) cc_final: 0.7719 (m-10) REVERT: A 24 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8122 (mtmt) REVERT: A 213 ILE cc_start: 0.8119 (tp) cc_final: 0.7797 (tp) REVERT: A 277 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 304 ILE cc_start: 0.7890 (mt) cc_final: 0.7644 (mt) REVERT: A 323 MET cc_start: 0.7093 (mmm) cc_final: 0.6563 (tmm) REVERT: A 336 PHE cc_start: 0.8445 (t80) cc_final: 0.7912 (t80) REVERT: B 32 GLN cc_start: 0.7466 (mt0) cc_final: 0.6921 (mt0) REVERT: B 48 ARG cc_start: 0.8402 (mmt90) cc_final: 0.8104 (mmt180) REVERT: B 49 ARG cc_start: 0.8702 (mmt-90) cc_final: 0.8421 (mmt180) REVERT: B 220 GLN cc_start: 0.8507 (mt0) cc_final: 0.7792 (mt0) REVERT: G 47 GLU cc_start: 0.7723 (mp0) cc_final: 0.7462 (mp0) REVERT: H 18 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7524 (ttm-80) REVERT: H 77 ASN cc_start: 0.7546 (m-40) cc_final: 0.7312 (m-40) REVERT: H 176 TRP cc_start: 0.8595 (m100) cc_final: 0.7889 (m100) REVERT: H 215 THR cc_start: 0.8590 (m) cc_final: 0.8149 (p) REVERT: H 219 LEU cc_start: 0.8138 (tp) cc_final: 0.7783 (tp) REVERT: H 227 TYR cc_start: 0.6749 (m-80) cc_final: 0.6443 (m-80) REVERT: H 237 LEU cc_start: 0.8584 (mt) cc_final: 0.8332 (mp) outliers start: 16 outliers final: 15 residues processed: 239 average time/residue: 0.1175 time to fit residues: 36.4860 Evaluate side-chains 235 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 74 optimal weight: 0.3980 chunk 62 optimal weight: 0.0570 chunk 4 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 179 GLN ** 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 = 0.3820 r_free = 0.3820 target = 0.137601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116630 restraints weight = 12896.031| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.00 r_work: 0.3425 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8390 Z= 0.121 Angle : 0.502 8.376 11456 Z= 0.267 Chirality : 0.042 0.150 1344 Planarity : 0.004 0.041 1459 Dihedral : 3.962 26.223 1194 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 14.83 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 1106 helix: 2.22 (0.27), residues: 398 sheet: -0.36 (0.33), residues: 245 loop : -0.32 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 198 TYR 0.019 0.001 TYR H 190 PHE 0.010 0.001 PHE B 199 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8387) covalent geometry : angle 0.50193 (11450) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.53539 ( 6) hydrogen bonds : bond 0.03551 ( 451) hydrogen bonds : angle 5.27037 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 TYR cc_start: 0.7175 (m-80) cc_final: 0.6807 (m-80) REVERT: C 423 PHE cc_start: 0.7912 (m-10) cc_final: 0.7663 (m-10) REVERT: A 24 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8114 (mtmt) REVERT: A 213 ILE cc_start: 0.8114 (tp) cc_final: 0.7778 (tp) REVERT: A 258 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8316 (ttpp) REVERT: A 277 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 304 ILE cc_start: 0.7963 (mt) cc_final: 0.7742 (mt) REVERT: A 336 PHE cc_start: 0.8411 (t80) cc_final: 0.7861 (t80) REVERT: B 32 GLN cc_start: 0.7486 (mt0) cc_final: 0.7000 (mt0) REVERT: B 68 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7964 (ttt180) REVERT: B 90 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 175 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7644 (mm-40) REVERT: B 220 GLN cc_start: 0.8507 (mt0) cc_final: 0.7915 (mt0) REVERT: G 47 GLU cc_start: 0.7748 (mp0) cc_final: 0.7450 (mp0) REVERT: H 7 SER cc_start: 0.7212 (t) cc_final: 0.6976 (m) REVERT: H 18 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7584 (ttm-80) REVERT: H 176 TRP cc_start: 0.8569 (m100) cc_final: 0.7902 (m100) REVERT: H 215 THR cc_start: 0.8594 (m) cc_final: 0.8314 (p) REVERT: H 219 LEU cc_start: 0.8158 (tp) cc_final: 0.7835 (tp) REVERT: H 230 MET cc_start: 0.8345 (ttp) cc_final: 0.8116 (ttp) REVERT: H 237 LEU cc_start: 0.8577 (mt) cc_final: 0.8318 (mp) outliers start: 18 outliers final: 12 residues processed: 222 average time/residue: 0.1279 time to fit residues: 36.2480 Evaluate side-chains 224 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 179 GLN ** 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 = 0.3804 r_free = 0.3804 target = 0.136457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115027 restraints weight = 13172.677| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.14 r_work: 0.3392 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8390 Z= 0.164 Angle : 0.524 8.036 11456 Z= 0.280 Chirality : 0.043 0.154 1344 Planarity : 0.004 0.042 1459 Dihedral : 4.084 30.895 1194 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.79 % Allowed : 14.96 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 1106 helix: 2.15 (0.27), residues: 396 sheet: -0.54 (0.32), residues: 251 loop : -0.26 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.021 0.002 TYR H 190 PHE 0.016 0.001 PHE C 69 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8387) covalent geometry : angle 0.52397 (11450) SS BOND : bond 0.00426 ( 3) SS BOND : angle 1.02469 ( 6) hydrogen bonds : bond 0.03561 ( 451) hydrogen bonds : angle 5.18904 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: C 110 VAL cc_start: 0.7482 (p) cc_final: 0.7160 (t) REVERT: C 160 TYR cc_start: 0.7251 (m-80) cc_final: 0.6868 (m-80) REVERT: A 24 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8097 (mtmt) REVERT: A 213 ILE cc_start: 0.8164 (tp) cc_final: 0.7851 (tp) REVERT: A 252 ASP cc_start: 0.7945 (t0) cc_final: 0.7713 (t0) REVERT: A 258 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: A 277 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 336 PHE cc_start: 0.8468 (t80) cc_final: 0.7867 (t80) REVERT: B 32 GLN cc_start: 0.7481 (mt0) cc_final: 0.6936 (mt0) REVERT: B 68 ARG cc_start: 0.8200 (ttt180) cc_final: 0.7947 (ttt180) REVERT: B 90 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 127 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8783 (mmtp) REVERT: B 220 GLN cc_start: 0.8561 (mt0) cc_final: 0.8066 (mt0) REVERT: B 258 ASP cc_start: 0.7533 (t70) cc_final: 0.7111 (t70) REVERT: B 259 GLN cc_start: 0.8335 (pm20) cc_final: 0.7908 (pm20) REVERT: G 47 GLU cc_start: 0.7550 (mp0) cc_final: 0.7205 (mp0) REVERT: H 7 SER cc_start: 0.7254 (t) cc_final: 0.7000 (m) REVERT: H 18 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7502 (ttm170) REVERT: H 176 TRP cc_start: 0.8560 (m100) cc_final: 0.7863 (m100) REVERT: H 215 THR cc_start: 0.8598 (m) cc_final: 0.8329 (p) REVERT: H 219 LEU cc_start: 0.8212 (tp) cc_final: 0.7895 (tp) REVERT: H 230 MET cc_start: 0.8361 (ttp) cc_final: 0.8150 (ttp) outliers start: 22 outliers final: 15 residues processed: 228 average time/residue: 0.1225 time to fit residues: 36.0500 Evaluate side-chains 235 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.138565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117256 restraints weight = 12853.656| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.04 r_work: 0.3402 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8390 Z= 0.161 Angle : 0.526 8.364 11456 Z= 0.278 Chirality : 0.043 0.155 1344 Planarity : 0.004 0.041 1459 Dihedral : 4.096 33.704 1194 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.17 % Allowed : 16.73 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1106 helix: 2.15 (0.26), residues: 397 sheet: -0.55 (0.32), residues: 262 loop : -0.23 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 365 TYR 0.018 0.002 TYR H 190 PHE 0.012 0.001 PHE B 278 TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8387) covalent geometry : angle 0.52541 (11450) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.86311 ( 6) hydrogen bonds : bond 0.03516 ( 451) hydrogen bonds : angle 5.10785 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 52 MET cc_start: 0.7037 (mmp) cc_final: 0.6663 (mmm) REVERT: C 110 VAL cc_start: 0.7442 (p) cc_final: 0.7134 (t) REVERT: C 160 TYR cc_start: 0.7701 (m-80) cc_final: 0.7208 (m-80) REVERT: C 365 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7339 (ttm110) REVERT: A 24 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8098 (mtmt) REVERT: A 26 ASP cc_start: 0.7995 (m-30) cc_final: 0.7792 (m-30) REVERT: A 213 ILE cc_start: 0.8168 (tp) cc_final: 0.7864 (tp) REVERT: A 252 ASP cc_start: 0.8085 (t0) cc_final: 0.7849 (t0) REVERT: A 258 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8289 (ttpp) REVERT: A 277 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 336 PHE cc_start: 0.8463 (t80) cc_final: 0.7630 (t80) REVERT: B 32 GLN cc_start: 0.7499 (mt0) cc_final: 0.7201 (mt0) REVERT: B 68 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7950 (ttt180) REVERT: B 90 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8223 (p) REVERT: B 127 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8780 (mmtp) REVERT: B 175 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7767 (mm-40) REVERT: B 259 GLN cc_start: 0.8298 (pm20) cc_final: 0.7909 (pm20) REVERT: B 323 ASP cc_start: 0.7617 (p0) cc_final: 0.7299 (p0) REVERT: G 47 GLU cc_start: 0.7546 (mp0) cc_final: 0.7164 (mp0) REVERT: H 18 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7287 (ttm170) REVERT: H 176 TRP cc_start: 0.8538 (m100) cc_final: 0.7969 (m100) REVERT: H 215 THR cc_start: 0.8556 (m) cc_final: 0.8295 (p) REVERT: H 219 LEU cc_start: 0.8230 (tp) cc_final: 0.7920 (tp) outliers start: 25 outliers final: 19 residues processed: 232 average time/residue: 0.1197 time to fit residues: 35.9188 Evaluate side-chains 238 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117865 restraints weight = 12911.065| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.08 r_work: 0.3397 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8390 Z= 0.160 Angle : 0.533 8.439 11456 Z= 0.281 Chirality : 0.043 0.160 1344 Planarity : 0.004 0.043 1459 Dihedral : 4.115 34.947 1194 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.42 % Allowed : 18.25 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.27), residues: 1106 helix: 2.18 (0.27), residues: 396 sheet: -0.57 (0.32), residues: 262 loop : -0.19 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.018 0.001 TYR H 190 PHE 0.019 0.001 PHE C 69 TRP 0.020 0.001 TRP B 169 HIS 0.004 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8387) covalent geometry : angle 0.53315 (11450) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.85479 ( 6) hydrogen bonds : bond 0.03460 ( 451) hydrogen bonds : angle 5.08022 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.326 Fit side-chains REVERT: C 160 TYR cc_start: 0.7746 (m-80) cc_final: 0.7085 (m-80) REVERT: A 24 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8075 (mtmt) REVERT: A 46 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7324 (mtmm) REVERT: A 213 ILE cc_start: 0.8185 (tp) cc_final: 0.7891 (tp) REVERT: A 258 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8297 (ttpp) REVERT: A 277 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 336 PHE cc_start: 0.8480 (t80) cc_final: 0.7774 (t80) REVERT: B 32 GLN cc_start: 0.7507 (mt0) cc_final: 0.7204 (mt0) REVERT: B 68 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7986 (ttt180) REVERT: B 90 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 175 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 219 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7594 (mtp85) REVERT: B 220 GLN cc_start: 0.8602 (mt0) cc_final: 0.7858 (mt0) REVERT: B 259 GLN cc_start: 0.8279 (pm20) cc_final: 0.7963 (pm20) REVERT: G 47 GLU cc_start: 0.7597 (mp0) cc_final: 0.7157 (mp0) REVERT: H 18 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7441 (ttm170) REVERT: H 176 TRP cc_start: 0.8521 (m100) cc_final: 0.7974 (m100) REVERT: H 215 THR cc_start: 0.8526 (m) cc_final: 0.8275 (p) REVERT: H 219 LEU cc_start: 0.8235 (tp) cc_final: 0.7937 (tp) outliers start: 27 outliers final: 22 residues processed: 231 average time/residue: 0.1237 time to fit residues: 36.8586 Evaluate side-chains 243 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114420 restraints weight = 13054.329| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.02 r_work: 0.3393 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8390 Z= 0.196 Angle : 0.564 8.326 11456 Z= 0.296 Chirality : 0.044 0.162 1344 Planarity : 0.004 0.047 1459 Dihedral : 4.247 35.991 1194 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.42 % Allowed : 19.26 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 1106 helix: 2.12 (0.26), residues: 396 sheet: -0.65 (0.32), residues: 262 loop : -0.21 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 365 TYR 0.020 0.002 TYR H 60 PHE 0.020 0.002 PHE B 199 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8387) covalent geometry : angle 0.56371 (11450) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.90271 ( 6) hydrogen bonds : bond 0.03602 ( 451) hydrogen bonds : angle 5.11291 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: C 160 TYR cc_start: 0.7764 (m-80) cc_final: 0.7253 (m-80) REVERT: C 173 ARG cc_start: 0.5552 (tmt170) cc_final: 0.5220 (tmt170) REVERT: C 365 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7245 (ttm110) REVERT: A 24 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8085 (mtmt) REVERT: A 46 LYS cc_start: 0.7681 (mtmt) cc_final: 0.7422 (mtmm) REVERT: A 213 ILE cc_start: 0.8186 (tp) cc_final: 0.7893 (tp) REVERT: A 252 ASP cc_start: 0.7948 (t0) cc_final: 0.7707 (t0) REVERT: A 258 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8273 (ttpp) REVERT: A 277 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 309 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 336 PHE cc_start: 0.8504 (t80) cc_final: 0.7578 (t80) REVERT: B 32 GLN cc_start: 0.7505 (mt0) cc_final: 0.7218 (mt0) REVERT: B 90 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (p) REVERT: B 175 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7645 (mm-40) REVERT: B 259 GLN cc_start: 0.8255 (pm20) cc_final: 0.7982 (pm20) REVERT: G 47 GLU cc_start: 0.7656 (mp0) cc_final: 0.7148 (mp0) REVERT: H 18 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7325 (ttm170) REVERT: H 176 TRP cc_start: 0.8527 (m100) cc_final: 0.8000 (m100) REVERT: H 215 THR cc_start: 0.8523 (m) cc_final: 0.8279 (p) REVERT: H 219 LEU cc_start: 0.8251 (tp) cc_final: 0.7966 (tp) outliers start: 27 outliers final: 21 residues processed: 233 average time/residue: 0.1231 time to fit residues: 36.9839 Evaluate side-chains 249 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.0770 chunk 4 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118864 restraints weight = 12918.463| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.07 r_work: 0.3413 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8390 Z= 0.129 Angle : 0.540 8.845 11456 Z= 0.278 Chirality : 0.043 0.148 1344 Planarity : 0.004 0.045 1459 Dihedral : 4.097 35.666 1194 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.30 % Allowed : 20.15 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 1106 helix: 2.20 (0.26), residues: 396 sheet: -0.65 (0.31), residues: 273 loop : -0.16 (0.33), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 365 TYR 0.020 0.002 TYR H 60 PHE 0.023 0.001 PHE C 69 TRP 0.022 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8387) covalent geometry : angle 0.53995 (11450) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.78610 ( 6) hydrogen bonds : bond 0.03337 ( 451) hydrogen bonds : angle 4.99512 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.294 Fit side-chains REVERT: C 52 MET cc_start: 0.7107 (mmp) cc_final: 0.6697 (mmm) REVERT: C 160 TYR cc_start: 0.7751 (m-80) cc_final: 0.7273 (m-80) REVERT: C 173 ARG cc_start: 0.5491 (tmt170) cc_final: 0.5176 (tmt170) REVERT: A 24 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8097 (mtmt) REVERT: A 46 LYS cc_start: 0.7629 (mtmt) cc_final: 0.7362 (mtmm) REVERT: A 213 ILE cc_start: 0.8183 (tp) cc_final: 0.7895 (tp) REVERT: A 258 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8248 (ttpp) REVERT: A 277 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 309 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 336 PHE cc_start: 0.8454 (t80) cc_final: 0.7600 (t80) REVERT: B 32 GLN cc_start: 0.7520 (mt0) cc_final: 0.7233 (mt0) REVERT: B 90 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (p) REVERT: B 150 ARG cc_start: 0.8498 (mmt180) cc_final: 0.7970 (mpt180) REVERT: B 175 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7609 (mm-40) REVERT: B 219 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7352 (mtp85) REVERT: B 220 GLN cc_start: 0.8455 (mt0) cc_final: 0.8167 (mt0) REVERT: B 258 ASP cc_start: 0.7450 (t70) cc_final: 0.7179 (t70) REVERT: B 259 GLN cc_start: 0.8182 (pm20) cc_final: 0.7861 (pm20) REVERT: G 47 GLU cc_start: 0.7637 (mp0) cc_final: 0.7116 (mp0) REVERT: H 18 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7220 (ttm170) REVERT: H 176 TRP cc_start: 0.8496 (m100) cc_final: 0.7937 (m100) REVERT: H 215 THR cc_start: 0.8505 (m) cc_final: 0.8266 (p) REVERT: H 219 LEU cc_start: 0.8226 (tp) cc_final: 0.7938 (tp) outliers start: 26 outliers final: 22 residues processed: 231 average time/residue: 0.1290 time to fit residues: 37.9286 Evaluate side-chains 240 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.0000 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119882 restraints weight = 12909.091| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.07 r_work: 0.3425 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8390 Z= 0.117 Angle : 0.531 9.066 11456 Z= 0.273 Chirality : 0.042 0.152 1344 Planarity : 0.004 0.044 1459 Dihedral : 4.004 36.594 1194 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.92 % Allowed : 21.29 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 1106 helix: 2.27 (0.26), residues: 397 sheet: -0.65 (0.31), residues: 279 loop : -0.10 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 365 TYR 0.019 0.001 TYR H 60 PHE 0.020 0.001 PHE C 69 TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8387) covalent geometry : angle 0.53064 (11450) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.77082 ( 6) hydrogen bonds : bond 0.03231 ( 451) hydrogen bonds : angle 4.89972 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.269 Fit side-chains REVERT: C 52 MET cc_start: 0.7090 (mmp) cc_final: 0.6559 (mmm) REVERT: C 110 VAL cc_start: 0.7430 (p) cc_final: 0.7088 (t) REVERT: C 160 TYR cc_start: 0.7726 (m-80) cc_final: 0.7120 (m-80) REVERT: C 173 ARG cc_start: 0.5464 (tmt170) cc_final: 0.5138 (tmt170) REVERT: C 365 ARG cc_start: 0.7494 (ttm110) cc_final: 0.6753 (mtt180) REVERT: A 24 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8110 (mtmt) REVERT: A 213 ILE cc_start: 0.8183 (tp) cc_final: 0.7888 (tp) REVERT: A 258 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8219 (ttpp) REVERT: A 277 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 336 PHE cc_start: 0.8429 (t80) cc_final: 0.7682 (t80) REVERT: B 90 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8109 (p) REVERT: B 127 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8586 (mttm) REVERT: B 150 ARG cc_start: 0.8481 (mmt180) cc_final: 0.7927 (mpt180) REVERT: B 175 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7653 (mm-40) REVERT: B 219 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7083 (mtp85) REVERT: B 220 GLN cc_start: 0.8430 (mt0) cc_final: 0.8086 (mt0) REVERT: B 258 ASP cc_start: 0.7428 (t70) cc_final: 0.6889 (t70) REVERT: B 259 GLN cc_start: 0.8148 (pm20) cc_final: 0.7865 (pm20) REVERT: B 339 TRP cc_start: 0.8329 (m100) cc_final: 0.7750 (m100) REVERT: G 47 GLU cc_start: 0.7620 (mp0) cc_final: 0.7121 (mp0) REVERT: H 18 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7193 (ttm170) REVERT: H 176 TRP cc_start: 0.8471 (m100) cc_final: 0.8011 (m100) REVERT: H 215 THR cc_start: 0.8500 (m) cc_final: 0.8274 (p) REVERT: H 219 LEU cc_start: 0.8185 (tp) cc_final: 0.7903 (tp) REVERT: H 227 TYR cc_start: 0.6609 (m-80) cc_final: 0.6345 (m-80) outliers start: 23 outliers final: 20 residues processed: 221 average time/residue: 0.1279 time to fit residues: 35.9103 Evaluate side-chains 233 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118368 restraints weight = 12872.920| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.07 r_work: 0.3406 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8390 Z= 0.163 Angle : 0.559 8.684 11456 Z= 0.289 Chirality : 0.044 0.184 1344 Planarity : 0.004 0.045 1459 Dihedral : 4.101 37.643 1194 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.92 % Allowed : 22.18 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 1106 helix: 2.19 (0.26), residues: 396 sheet: -0.63 (0.31), residues: 279 loop : -0.13 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 365 TYR 0.018 0.002 TYR H 235 PHE 0.018 0.001 PHE C 69 TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8387) covalent geometry : angle 0.55887 (11450) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.84377 ( 6) hydrogen bonds : bond 0.03466 ( 451) hydrogen bonds : angle 4.97461 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.219 Fit side-chains REVERT: C 52 MET cc_start: 0.7090 (mmp) cc_final: 0.6555 (mmm) REVERT: C 110 VAL cc_start: 0.7366 (p) cc_final: 0.7068 (t) REVERT: C 148 VAL cc_start: 0.8435 (t) cc_final: 0.8234 (m) REVERT: C 160 TYR cc_start: 0.7750 (m-80) cc_final: 0.7125 (m-80) REVERT: C 173 ARG cc_start: 0.5523 (tmt170) cc_final: 0.5189 (tmt170) REVERT: C 365 ARG cc_start: 0.7508 (ttm110) cc_final: 0.6674 (mtt180) REVERT: A 21 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8452 (ttmm) REVERT: A 24 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8169 (mtmt) REVERT: A 213 ILE cc_start: 0.8185 (tp) cc_final: 0.7898 (tp) REVERT: A 258 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8255 (ttpp) REVERT: A 277 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 309 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6986 (tm-30) REVERT: A 336 PHE cc_start: 0.8464 (t80) cc_final: 0.7591 (t80) REVERT: B 32 GLN cc_start: 0.7298 (mt0) cc_final: 0.6996 (mp10) REVERT: B 90 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 150 ARG cc_start: 0.8498 (mmt180) cc_final: 0.7986 (mpt180) REVERT: B 175 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7650 (mm-40) REVERT: B 219 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7498 (ttm110) REVERT: B 258 ASP cc_start: 0.7475 (t70) cc_final: 0.7219 (t70) REVERT: B 259 GLN cc_start: 0.8192 (pm20) cc_final: 0.7880 (pm20) REVERT: B 339 TRP cc_start: 0.8347 (m100) cc_final: 0.7682 (m100) REVERT: G 47 GLU cc_start: 0.7652 (mp0) cc_final: 0.7127 (mp0) REVERT: H 18 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7207 (ttm170) REVERT: H 59 TYR cc_start: 0.7522 (m-10) cc_final: 0.7174 (m-80) REVERT: H 176 TRP cc_start: 0.8478 (m100) cc_final: 0.8065 (m100) REVERT: H 215 THR cc_start: 0.8499 (m) cc_final: 0.8270 (p) REVERT: H 219 LEU cc_start: 0.8179 (tp) cc_final: 0.7905 (tp) REVERT: H 227 TYR cc_start: 0.6628 (m-80) cc_final: 0.6340 (m-80) outliers start: 23 outliers final: 19 residues processed: 230 average time/residue: 0.1205 time to fit residues: 35.4664 Evaluate side-chains 240 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115392 restraints weight = 12993.314| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.01 r_work: 0.3407 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8390 Z= 0.183 Angle : 0.578 8.462 11456 Z= 0.299 Chirality : 0.045 0.199 1344 Planarity : 0.004 0.045 1459 Dihedral : 4.226 37.509 1194 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.04 % Allowed : 22.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.27), residues: 1106 helix: 2.13 (0.26), residues: 396 sheet: -0.64 (0.31), residues: 279 loop : -0.17 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 365 TYR 0.026 0.002 TYR H 235 PHE 0.018 0.002 PHE H 239 TRP 0.019 0.002 TRP B 211 HIS 0.004 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8387) covalent geometry : angle 0.57775 (11450) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.88076 ( 6) hydrogen bonds : bond 0.03641 ( 451) hydrogen bonds : angle 5.04775 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2602.13 seconds wall clock time: 45 minutes 28.19 seconds (2728.19 seconds total)