Starting phenix.real_space_refine on Wed Feb 4 05:23:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l42_62803/02_2026/9l42_62803.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l42_62803/02_2026/9l42_62803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l42_62803/02_2026/9l42_62803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l42_62803/02_2026/9l42_62803.map" model { file = "/net/cci-nas-00/data/ceres_data/9l42_62803/02_2026/9l42_62803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l42_62803/02_2026/9l42_62803.cif" } resolution = 2.9 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= 0.001 sd= 0.026 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 57 5.16 5 C 5630 2.51 5 N 1475 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 8762 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2205 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1745 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.99, per 1000 atoms: 0.23 Number of scatterers: 8762 At special positions: 0 Unit cell: (85.56, 119.04, 120.9, 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 57 16.00 O 1600 8.00 N 1475 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 0.73 Conformation dependent library (CDL) restraints added in 329.3 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.9% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 16 through 43 Processing helix chain 'A' and resid 48 through 67 removed outlier: 3.822A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.707A pdb=" N LEU A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 118 removed outlier: 4.592A pdb=" N THR A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 128 through 154 removed outlier: 3.584A pdb=" N TRP A 140 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.501A pdb=" N SER A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.554A pdb=" N LEU A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 330 Proline residue: A 318 - end of helix Processing helix chain 'A' and resid 337 through 362 removed outlier: 3.875A pdb=" N TRP A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Proline residue: A 355 - end of helix Proline residue: A 359 - end of helix removed outlier: 3.690A pdb=" N HIS A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.346A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 removed outlier: 3.860A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.257A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.570A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.827A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 8 through 25 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.861A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.568A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.568A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.012A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.108A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.208A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.612A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.374A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.513A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.732A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.032A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.582A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.582A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1308 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: 1.49 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1396 1.30 - 1.43: 2461 1.43 - 1.55: 5022 1.55 - 1.68: 0 1.68 - 1.81: 83 Bond restraints: 8962 Sorted by residual: bond pdb=" CA LEU C 336 " pdb=" C LEU C 336 " ideal model delta sigma weight residual 1.522 1.433 0.089 1.22e-02 6.72e+03 5.33e+01 bond pdb=" CA LYS C 337 " pdb=" C LYS C 337 " ideal model delta sigma weight residual 1.520 1.443 0.077 1.20e-02 6.94e+03 4.10e+01 bond pdb=" C LYS C 337 " pdb=" O LYS C 337 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.11e-02 8.12e+03 3.16e+01 bond pdb=" CA PHE C 335 " pdb=" C PHE C 335 " ideal model delta sigma weight residual 1.520 1.458 0.063 1.22e-02 6.72e+03 2.65e+01 bond pdb=" CA TRP A 348 " pdb=" C TRP A 348 " ideal model delta sigma weight residual 1.519 1.452 0.067 1.32e-02 5.74e+03 2.61e+01 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11849 2.64 - 5.28: 269 5.28 - 7.92: 35 7.92 - 10.56: 12 10.56 - 13.20: 2 Bond angle restraints: 12167 Sorted by residual: angle pdb=" N ASP A 81 " pdb=" CA ASP A 81 " pdb=" C ASP A 81 " ideal model delta sigma weight residual 112.03 98.83 13.20 1.31e+00 5.83e-01 1.01e+02 angle pdb=" N LEU A 96 " pdb=" CA LEU A 96 " pdb=" C LEU A 96 " ideal model delta sigma weight residual 112.72 101.68 11.04 1.28e+00 6.10e-01 7.43e+01 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 110.72 102.85 7.87 1.01e+00 9.80e-01 6.08e+01 angle pdb=" N TRP A 348 " pdb=" CA TRP A 348 " pdb=" C TRP A 348 " ideal model delta sigma weight residual 113.88 105.02 8.86 1.23e+00 6.61e-01 5.19e+01 angle pdb=" C VAL B 201 " pdb=" CA VAL B 201 " pdb=" CB VAL B 201 " ideal model delta sigma weight residual 112.46 103.03 9.43 1.33e+00 5.65e-01 5.03e+01 ... (remaining 12162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 4867 14.57 - 29.13: 340 29.13 - 43.70: 70 43.70 - 58.26: 21 58.26 - 72.83: 6 Dihedral angle restraints: 5304 sinusoidal: 2031 harmonic: 3273 Sorted by residual: dihedral pdb=" CB CYS A 87 " pdb=" SG CYS A 87 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual -86.00 -146.95 60.95 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" C ARG E 179 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " pdb=" CB ARG E 179 " ideal model delta harmonic sigma weight residual -122.60 -135.03 12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C TYR A 358 " pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" CB TYR A 358 " ideal model delta harmonic sigma weight residual -122.60 -134.65 12.05 0 2.50e+00 1.60e-01 2.32e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1258 0.110 - 0.220: 110 0.220 - 0.330: 13 0.330 - 0.440: 1 0.440 - 0.550: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ARG E 179 " pdb=" N ARG E 179 " pdb=" C ARG E 179 " pdb=" CB ARG E 179 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CA THR A 76 " pdb=" N THR A 76 " pdb=" C THR A 76 " pdb=" CB THR A 76 " both_signs ideal model delta sigma weight residual False 2.53 2.01 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CA TYR A 358 " pdb=" N TYR A 358 " pdb=" C TYR A 358 " pdb=" CB TYR A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 1383 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 200 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C ASP B 200 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 200 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 334 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C SER C 334 " -0.043 2.00e-02 2.50e+03 pdb=" O SER C 334 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE C 335 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 185 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 186 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " 0.036 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1003 2.74 - 3.28: 8738 3.28 - 3.82: 14837 3.82 - 4.36: 18605 4.36 - 4.90: 31624 Nonbonded interactions: 74807 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.199 3.040 nonbonded pdb=" ND2 ASN C 230 " pdb=" OD1 ASP C 246 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG E 67 " pdb=" O SER E 85 " model vdw 2.292 3.120 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN E 130 " pdb=" O ALA E 229 " model vdw 2.332 3.120 ... (remaining 74802 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 8965 Z= 0.612 Angle : 0.950 13.197 12173 Z= 0.624 Chirality : 0.071 0.550 1386 Planarity : 0.005 0.061 1522 Dihedral : 11.087 72.825 3181 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 7.48 % Favored : 91.43 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.45 % 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: -0.15 (0.25), residues: 1107 helix: 0.01 (0.25), residues: 390 sheet: 0.14 (0.30), residues: 261 loop : -0.13 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.023 0.002 TYR E 178 PHE 0.025 0.002 PHE B 354 TRP 0.015 0.002 TRP C 169 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00861 ( 8962) covalent geometry : angle 0.95062 (12167) SS BOND : bond 0.00704 ( 3) SS BOND : angle 0.52588 ( 6) hydrogen bonds : bond 0.18212 ( 456) hydrogen bonds : angle 6.85879 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.366 Fit side-chains REVERT: A 43 ASP cc_start: 0.7887 (t0) cc_final: 0.7378 (t0) REVERT: A 47 ARG cc_start: 0.8840 (mmt90) cc_final: 0.8419 (mpt180) REVERT: A 94 ASP cc_start: 0.8758 (t0) cc_final: 0.8488 (t0) REVERT: A 154 SER cc_start: 0.8789 (m) cc_final: 0.8542 (p) REVERT: A 166 PRO cc_start: 0.8817 (Cg_exo) cc_final: 0.8505 (Cg_endo) REVERT: A 338 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8172 (p) REVERT: A 341 ARG cc_start: 0.7917 (mtt90) cc_final: 0.6749 (ttt180) REVERT: B 20 ASP cc_start: 0.8014 (t0) cc_final: 0.7607 (m-30) REVERT: B 24 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7337 (ttp80) REVERT: B 242 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8240 (mtt-85) REVERT: B 305 CYS cc_start: 0.8337 (m) cc_final: 0.7892 (t) REVERT: B 306 GLN cc_start: 0.8579 (mm-40) cc_final: 0.7884 (mp10) REVERT: C 46 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7433 (mtp85) REVERT: C 127 LYS cc_start: 0.9022 (mttm) cc_final: 0.8799 (mttm) REVERT: C 247 ASP cc_start: 0.7740 (t70) cc_final: 0.7508 (t70) REVERT: C 336 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9106 (mt) REVERT: D 17 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8748 (mm-30) REVERT: D 19 LEU cc_start: 0.8389 (mp) cc_final: 0.8148 (mp) REVERT: D 20 LYS cc_start: 0.9278 (ttpp) cc_final: 0.8641 (pttp) REVERT: D 31 SER cc_start: 0.8310 (t) cc_final: 0.8097 (p) REVERT: E 13 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8602 (mm110) REVERT: E 46 GLU cc_start: 0.8337 (tt0) cc_final: 0.8134 (tt0) REVERT: E 65 LYS cc_start: 0.8493 (tttp) cc_final: 0.8179 (ttpt) REVERT: E 143 VAL cc_start: 0.8131 (p) cc_final: 0.7900 (m) REVERT: E 151 LYS cc_start: 0.8671 (tttt) cc_final: 0.8446 (tttt) REVERT: E 222 GLU cc_start: 0.8726 (pt0) cc_final: 0.8427 (pt0) outliers start: 10 outliers final: 3 residues processed: 214 average time/residue: 0.5701 time to fit residues: 129.1301 Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PRO Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 26 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 125 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN B 311 ASN B 331 ASN C 32 GLN C 44 GLN C 75 GLN C 293 ASN C 295 ASN D 18 GLN E 130 GLN E 220 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081297 restraints weight = 13391.591| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.69 r_work: 0.2822 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8965 Z= 0.228 Angle : 0.599 6.953 12173 Z= 0.318 Chirality : 0.043 0.176 1386 Planarity : 0.004 0.041 1522 Dihedral : 6.214 66.068 1291 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.69 % Allowed : 13.45 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1107 helix: 1.49 (0.26), residues: 392 sheet: 0.17 (0.31), residues: 256 loop : -0.01 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 197 TYR 0.018 0.001 TYR E 178 PHE 0.014 0.002 PHE A 183 TRP 0.018 0.002 TRP A 345 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 8962) covalent geometry : angle 0.59880 (12167) SS BOND : bond 0.00204 ( 3) SS BOND : angle 1.24868 ( 6) hydrogen bonds : bond 0.04960 ( 456) hydrogen bonds : angle 5.01552 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.300 Fit side-chains REVERT: A 154 SER cc_start: 0.8655 (m) cc_final: 0.8346 (p) REVERT: B 9 ASP cc_start: 0.7941 (m-30) cc_final: 0.7651 (m-30) REVERT: B 20 ASP cc_start: 0.7807 (t0) cc_final: 0.7518 (m-30) REVERT: B 52 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6614 (mp10) REVERT: B 247 MET cc_start: 0.8287 (mtm) cc_final: 0.8076 (mtp) REVERT: B 305 CYS cc_start: 0.8405 (m) cc_final: 0.7953 (t) REVERT: B 306 GLN cc_start: 0.8655 (mm-40) cc_final: 0.7884 (mp10) REVERT: C 46 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7491 (mtp85) REVERT: C 247 ASP cc_start: 0.7836 (t70) cc_final: 0.7538 (t0) REVERT: C 260 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: D 17 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8810 (mm-30) REVERT: D 20 LYS cc_start: 0.9160 (ttpp) cc_final: 0.8792 (pptt) REVERT: D 22 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: D 31 SER cc_start: 0.8330 (t) cc_final: 0.8109 (p) REVERT: D 46 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8933 (mmtp) REVERT: E 13 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8569 (mm110) REVERT: E 46 GLU cc_start: 0.8523 (tt0) cc_final: 0.8225 (tt0) REVERT: E 65 LYS cc_start: 0.8497 (tttp) cc_final: 0.8125 (ttpt) REVERT: E 151 LYS cc_start: 0.8707 (tttt) cc_final: 0.8474 (tttt) REVERT: E 182 ASN cc_start: 0.8527 (m-40) cc_final: 0.8249 (m-40) REVERT: E 222 GLU cc_start: 0.8830 (pt0) cc_final: 0.8522 (pt0) outliers start: 34 outliers final: 11 residues processed: 173 average time/residue: 0.4652 time to fit residues: 85.7638 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.0010 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 44 GLN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083492 restraints weight = 13198.791| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.73 r_work: 0.2884 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8965 Z= 0.118 Angle : 0.534 11.252 12173 Z= 0.277 Chirality : 0.040 0.141 1386 Planarity : 0.004 0.039 1522 Dihedral : 5.505 63.043 1281 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.90 % Allowed : 15.51 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.02 (0.25), residues: 1107 helix: 1.89 (0.26), residues: 391 sheet: 0.34 (0.32), residues: 247 loop : -0.09 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.017 0.001 TYR E 178 PHE 0.011 0.001 PHE A 183 TRP 0.017 0.001 TRP A 345 HIS 0.002 0.000 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8962) covalent geometry : angle 0.53338 (12167) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.82244 ( 6) hydrogen bonds : bond 0.04033 ( 456) hydrogen bonds : angle 4.56261 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.213 Fit side-chains REVERT: A 130 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7961 (tm) REVERT: A 154 SER cc_start: 0.8501 (m) cc_final: 0.8270 (p) REVERT: B 9 ASP cc_start: 0.7962 (m-30) cc_final: 0.7577 (m-30) REVERT: B 20 ASP cc_start: 0.7793 (t0) cc_final: 0.7541 (m-30) REVERT: B 232 LEU cc_start: 0.8350 (mp) cc_final: 0.8037 (mp) REVERT: B 305 CYS cc_start: 0.8376 (m) cc_final: 0.7900 (t) REVERT: B 306 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7839 (mp10) REVERT: C 46 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7503 (mtp85) REVERT: C 215 GLU cc_start: 0.7732 (pt0) cc_final: 0.7288 (pp20) REVERT: C 217 MET cc_start: 0.8433 (mmm) cc_final: 0.8111 (mmm) REVERT: C 247 ASP cc_start: 0.7773 (t0) cc_final: 0.7450 (t0) REVERT: C 260 GLU cc_start: 0.8354 (pt0) cc_final: 0.8079 (tt0) REVERT: D 17 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8771 (mm-30) REVERT: D 20 LYS cc_start: 0.9213 (ttpp) cc_final: 0.8386 (tmtt) REVERT: D 21 MET cc_start: 0.8743 (mmm) cc_final: 0.8332 (mmm) REVERT: D 22 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: E 6 GLU cc_start: 0.7629 (mp0) cc_final: 0.7098 (mt-10) REVERT: E 13 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8592 (mm110) REVERT: E 46 GLU cc_start: 0.8490 (tt0) cc_final: 0.8196 (tt0) REVERT: E 52 SER cc_start: 0.8504 (t) cc_final: 0.7924 (p) REVERT: E 65 LYS cc_start: 0.8459 (tttp) cc_final: 0.8090 (ttpt) REVERT: E 151 LYS cc_start: 0.8731 (tttt) cc_final: 0.8455 (tttt) REVERT: E 182 ASN cc_start: 0.8531 (m-40) cc_final: 0.8263 (m-40) REVERT: E 222 GLU cc_start: 0.8828 (pt0) cc_final: 0.8470 (pt0) outliers start: 36 outliers final: 6 residues processed: 183 average time/residue: 0.4203 time to fit residues: 82.4276 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083293 restraints weight = 13342.091| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.68 r_work: 0.2867 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8965 Z= 0.142 Angle : 0.533 9.730 12173 Z= 0.277 Chirality : 0.041 0.156 1386 Planarity : 0.003 0.039 1522 Dihedral : 5.348 59.310 1281 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.34 % Allowed : 15.62 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.04 (0.25), residues: 1107 helix: 1.86 (0.26), residues: 393 sheet: 0.24 (0.32), residues: 258 loop : 0.04 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE C 199 TRP 0.015 0.001 TRP A 316 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8962) covalent geometry : angle 0.53330 (12167) SS BOND : bond 0.00169 ( 3) SS BOND : angle 0.84178 ( 6) hydrogen bonds : bond 0.03907 ( 456) hydrogen bonds : angle 4.45868 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8040 (t0) cc_final: 0.7762 (t0) REVERT: A 130 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8007 (tm) REVERT: A 154 SER cc_start: 0.8430 (m) cc_final: 0.8222 (p) REVERT: B 9 ASP cc_start: 0.7983 (m-30) cc_final: 0.7552 (m-30) REVERT: B 20 ASP cc_start: 0.7808 (t0) cc_final: 0.7509 (m-30) REVERT: B 305 CYS cc_start: 0.8305 (m) cc_final: 0.7765 (t) REVERT: C 46 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7853 (mtp85) REVERT: C 215 GLU cc_start: 0.7726 (pt0) cc_final: 0.7268 (pp20) REVERT: C 217 MET cc_start: 0.8388 (mmm) cc_final: 0.8076 (mmm) REVERT: C 228 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7588 (p0) REVERT: C 247 ASP cc_start: 0.7828 (t0) cc_final: 0.7505 (t0) REVERT: C 260 GLU cc_start: 0.8429 (pt0) cc_final: 0.8154 (tt0) REVERT: D 17 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8826 (mm-30) REVERT: D 20 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8671 (tmtt) REVERT: D 21 MET cc_start: 0.8732 (mmm) cc_final: 0.8458 (mmm) REVERT: D 22 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: E 13 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8618 (mm110) REVERT: E 46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8202 (tt0) REVERT: E 65 LYS cc_start: 0.8421 (tttp) cc_final: 0.8043 (ttpt) REVERT: E 151 LYS cc_start: 0.8716 (tttt) cc_final: 0.8463 (tttt) REVERT: E 182 ASN cc_start: 0.8460 (m-40) cc_final: 0.8240 (m-40) REVERT: E 222 GLU cc_start: 0.8838 (pt0) cc_final: 0.8576 (pt0) outliers start: 40 outliers final: 13 residues processed: 175 average time/residue: 0.5261 time to fit residues: 98.1210 Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080735 restraints weight = 13419.253| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.64 r_work: 0.2826 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8965 Z= 0.212 Angle : 0.569 9.894 12173 Z= 0.295 Chirality : 0.042 0.206 1386 Planarity : 0.004 0.038 1522 Dihedral : 5.375 59.050 1281 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.12 % Allowed : 17.03 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.91 (0.25), residues: 1107 helix: 1.71 (0.26), residues: 391 sheet: 0.17 (0.32), residues: 258 loop : 0.01 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.014 0.001 TYR E 178 PHE 0.012 0.001 PHE C 253 TRP 0.018 0.001 TRP A 316 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8962) covalent geometry : angle 0.56870 (12167) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.89756 ( 6) hydrogen bonds : bond 0.04126 ( 456) hydrogen bonds : angle 4.53013 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8040 (t0) cc_final: 0.7773 (t0) REVERT: A 94 ASP cc_start: 0.8897 (t0) cc_final: 0.8606 (t0) REVERT: A 130 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7978 (tm) REVERT: A 147 ASN cc_start: 0.8176 (m-40) cc_final: 0.7936 (m-40) REVERT: A 154 SER cc_start: 0.8458 (m) cc_final: 0.8201 (p) REVERT: B 9 ASP cc_start: 0.8073 (m-30) cc_final: 0.7635 (m-30) REVERT: B 20 ASP cc_start: 0.7958 (t0) cc_final: 0.7645 (m-30) REVERT: B 305 CYS cc_start: 0.8390 (m) cc_final: 0.7886 (t) REVERT: C 46 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8046 (mtp85) REVERT: C 217 MET cc_start: 0.8501 (mmm) cc_final: 0.8187 (mmm) REVERT: C 228 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.7714 (p0) REVERT: C 247 ASP cc_start: 0.7995 (t0) cc_final: 0.7696 (t0) REVERT: C 260 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: D 17 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8807 (mm-30) REVERT: D 20 LYS cc_start: 0.9215 (ttpp) cc_final: 0.8403 (tmtt) REVERT: D 21 MET cc_start: 0.8767 (mmm) cc_final: 0.8336 (mmm) REVERT: D 22 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: E 6 GLU cc_start: 0.7977 (mp0) cc_final: 0.7172 (mt-10) REVERT: E 13 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8582 (mm110) REVERT: E 46 GLU cc_start: 0.8552 (tt0) cc_final: 0.8301 (tt0) REVERT: E 65 LYS cc_start: 0.8435 (tttp) cc_final: 0.8062 (ttpt) REVERT: E 222 GLU cc_start: 0.8929 (pt0) cc_final: 0.8617 (pt0) outliers start: 38 outliers final: 18 residues processed: 164 average time/residue: 0.5288 time to fit residues: 92.5149 Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 32 GLN C 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.083595 restraints weight = 13293.860| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.68 r_work: 0.2866 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8965 Z= 0.120 Angle : 0.534 9.055 12173 Z= 0.273 Chirality : 0.041 0.270 1386 Planarity : 0.003 0.039 1522 Dihedral : 5.126 54.756 1281 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.82 % Allowed : 18.22 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.08 (0.25), residues: 1107 helix: 1.87 (0.26), residues: 395 sheet: 0.37 (0.33), residues: 252 loop : -0.00 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.017 0.001 TYR E 178 PHE 0.010 0.001 PHE C 199 TRP 0.015 0.001 TRP A 316 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8962) covalent geometry : angle 0.53370 (12167) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.64666 ( 6) hydrogen bonds : bond 0.03655 ( 456) hydrogen bonds : angle 4.35735 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8038 (t0) cc_final: 0.7744 (t0) REVERT: A 94 ASP cc_start: 0.8778 (t0) cc_final: 0.8498 (t0) REVERT: A 130 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8032 (tm) REVERT: A 147 ASN cc_start: 0.8160 (m-40) cc_final: 0.7944 (m-40) REVERT: A 154 SER cc_start: 0.8416 (m) cc_final: 0.8158 (p) REVERT: B 9 ASP cc_start: 0.7974 (m-30) cc_final: 0.7507 (m-30) REVERT: B 20 ASP cc_start: 0.7811 (t0) cc_final: 0.7520 (m-30) REVERT: B 24 ARG cc_start: 0.7355 (ttp80) cc_final: 0.7140 (ttm110) REVERT: B 305 CYS cc_start: 0.8295 (m) cc_final: 0.7799 (t) REVERT: C 46 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7858 (mtp85) REVERT: C 215 GLU cc_start: 0.7877 (pt0) cc_final: 0.7442 (pp20) REVERT: C 217 MET cc_start: 0.8377 (mmm) cc_final: 0.8066 (mmm) REVERT: C 228 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7668 (p0) REVERT: C 247 ASP cc_start: 0.7779 (t0) cc_final: 0.7458 (t0) REVERT: C 260 GLU cc_start: 0.8447 (pt0) cc_final: 0.8197 (tt0) REVERT: D 17 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8793 (mm-30) REVERT: D 20 LYS cc_start: 0.9236 (ttpp) cc_final: 0.8412 (tmtt) REVERT: D 21 MET cc_start: 0.8769 (mmm) cc_final: 0.8333 (mmm) REVERT: D 22 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: E 13 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8612 (mm110) REVERT: E 46 GLU cc_start: 0.8423 (tt0) cc_final: 0.8140 (tt0) REVERT: E 65 LYS cc_start: 0.8484 (tttp) cc_final: 0.8143 (ttpt) REVERT: E 151 LYS cc_start: 0.8780 (tttt) cc_final: 0.8526 (ttpt) REVERT: E 222 GLU cc_start: 0.8802 (pt0) cc_final: 0.8355 (pt0) outliers start: 26 outliers final: 11 residues processed: 164 average time/residue: 0.5563 time to fit residues: 97.2772 Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082569 restraints weight = 13274.805| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.69 r_work: 0.2856 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8965 Z= 0.142 Angle : 0.566 13.354 12173 Z= 0.286 Chirality : 0.041 0.285 1386 Planarity : 0.003 0.043 1522 Dihedral : 5.046 51.492 1281 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.71 % Allowed : 18.98 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.10 (0.25), residues: 1107 helix: 1.86 (0.26), residues: 396 sheet: 0.43 (0.33), residues: 247 loop : 0.00 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.014 0.001 TYR E 178 PHE 0.010 0.001 PHE C 199 TRP 0.016 0.001 TRP A 316 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8962) covalent geometry : angle 0.56598 (12167) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.78472 ( 6) hydrogen bonds : bond 0.03684 ( 456) hydrogen bonds : angle 4.33993 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7992 (t0) cc_final: 0.7723 (t0) REVERT: A 94 ASP cc_start: 0.8759 (t0) cc_final: 0.8456 (t0) REVERT: A 130 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8028 (tm) REVERT: A 154 SER cc_start: 0.8420 (m) cc_final: 0.8171 (p) REVERT: B 9 ASP cc_start: 0.7950 (m-30) cc_final: 0.7472 (m-30) REVERT: B 20 ASP cc_start: 0.7804 (t0) cc_final: 0.7498 (m-30) REVERT: B 24 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7103 (ttm110) REVERT: B 305 CYS cc_start: 0.8284 (m) cc_final: 0.7796 (t) REVERT: C 46 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7866 (mtp85) REVERT: C 215 GLU cc_start: 0.7870 (pt0) cc_final: 0.7422 (pp20) REVERT: C 217 MET cc_start: 0.8385 (mmm) cc_final: 0.8091 (mmm) REVERT: C 228 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7681 (p0) REVERT: C 247 ASP cc_start: 0.7751 (t0) cc_final: 0.7449 (t0) REVERT: C 260 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: D 17 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8784 (mm-30) REVERT: D 20 LYS cc_start: 0.9245 (ttpp) cc_final: 0.8428 (tmtt) REVERT: D 21 MET cc_start: 0.8772 (mmm) cc_final: 0.8330 (mmm) REVERT: E 6 GLU cc_start: 0.7723 (mp0) cc_final: 0.6766 (mt-10) REVERT: E 13 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8603 (mm110) REVERT: E 46 GLU cc_start: 0.8416 (tt0) cc_final: 0.8162 (tt0) REVERT: E 65 LYS cc_start: 0.8378 (tttp) cc_final: 0.8020 (ttpt) REVERT: E 151 LYS cc_start: 0.8762 (tttt) cc_final: 0.8542 (ttpt) REVERT: E 222 GLU cc_start: 0.8818 (pt0) cc_final: 0.8574 (pt0) outliers start: 25 outliers final: 11 residues processed: 160 average time/residue: 0.6100 time to fit residues: 103.8729 Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082449 restraints weight = 13243.941| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.63 r_work: 0.2852 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8965 Z= 0.159 Angle : 0.575 12.511 12173 Z= 0.291 Chirality : 0.042 0.289 1386 Planarity : 0.003 0.038 1522 Dihedral : 5.020 49.983 1281 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.71 % Allowed : 19.41 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.06 (0.25), residues: 1107 helix: 1.82 (0.26), residues: 397 sheet: 0.42 (0.33), residues: 247 loop : -0.03 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 208 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.001 PHE C 199 TRP 0.016 0.001 TRP A 316 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8962) covalent geometry : angle 0.57482 (12167) SS BOND : bond 0.00169 ( 3) SS BOND : angle 0.65490 ( 6) hydrogen bonds : bond 0.03770 ( 456) hydrogen bonds : angle 4.37164 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8013 (t0) cc_final: 0.7747 (t0) REVERT: A 94 ASP cc_start: 0.8835 (t0) cc_final: 0.8542 (t0) REVERT: A 130 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7993 (tm) REVERT: A 154 SER cc_start: 0.8407 (m) cc_final: 0.8129 (p) REVERT: B 9 ASP cc_start: 0.8070 (m-30) cc_final: 0.7615 (m-30) REVERT: B 20 ASP cc_start: 0.7939 (t0) cc_final: 0.7646 (m-30) REVERT: B 24 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7228 (ttm110) REVERT: B 305 CYS cc_start: 0.8393 (m) cc_final: 0.7894 (t) REVERT: C 46 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8061 (mtp85) REVERT: C 215 GLU cc_start: 0.7882 (pt0) cc_final: 0.7426 (pp20) REVERT: C 217 MET cc_start: 0.8547 (mmm) cc_final: 0.8226 (mmm) REVERT: C 228 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7778 (p0) REVERT: C 247 ASP cc_start: 0.7918 (t0) cc_final: 0.7614 (t0) REVERT: C 260 GLU cc_start: 0.8587 (pt0) cc_final: 0.8331 (tt0) REVERT: D 17 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8786 (mm-30) REVERT: D 20 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8398 (tmtt) REVERT: D 21 MET cc_start: 0.8777 (mmm) cc_final: 0.8348 (mmm) REVERT: D 22 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: D 47 GLU cc_start: 0.8482 (mp0) cc_final: 0.8079 (mp0) REVERT: E 13 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8592 (mm110) REVERT: E 46 GLU cc_start: 0.8576 (tt0) cc_final: 0.8330 (tt0) REVERT: E 65 LYS cc_start: 0.8400 (tttp) cc_final: 0.8033 (ttpt) REVERT: E 151 LYS cc_start: 0.8776 (tttt) cc_final: 0.8559 (ttpt) REVERT: E 222 GLU cc_start: 0.8935 (pt0) cc_final: 0.8717 (pt0) outliers start: 25 outliers final: 13 residues processed: 154 average time/residue: 0.5742 time to fit residues: 94.0495 Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082462 restraints weight = 13200.375| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.73 r_work: 0.2861 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8965 Z= 0.136 Angle : 0.566 12.389 12173 Z= 0.286 Chirality : 0.041 0.294 1386 Planarity : 0.003 0.038 1522 Dihedral : 4.910 46.817 1281 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 19.96 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.07 (0.25), residues: 1107 helix: 1.84 (0.26), residues: 397 sheet: 0.42 (0.33), residues: 247 loop : -0.03 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 208 TYR 0.012 0.001 TYR E 178 PHE 0.010 0.001 PHE C 199 TRP 0.019 0.001 TRP A 316 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8962) covalent geometry : angle 0.56546 (12167) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.65133 ( 6) hydrogen bonds : bond 0.03654 ( 456) hydrogen bonds : angle 4.32692 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8144 (mm) cc_final: 0.7825 (tt) REVERT: A 43 ASP cc_start: 0.8000 (t0) cc_final: 0.7735 (t0) REVERT: A 94 ASP cc_start: 0.8749 (t0) cc_final: 0.8440 (t0) REVERT: A 130 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8034 (tm) REVERT: A 154 SER cc_start: 0.8414 (m) cc_final: 0.8131 (p) REVERT: B 9 ASP cc_start: 0.7946 (m-30) cc_final: 0.7466 (m-30) REVERT: B 20 ASP cc_start: 0.7790 (t0) cc_final: 0.7481 (m-30) REVERT: B 24 ARG cc_start: 0.7342 (ttp80) cc_final: 0.7109 (ttm110) REVERT: B 305 CYS cc_start: 0.8297 (m) cc_final: 0.7817 (t) REVERT: C 23 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8765 (ttpp) REVERT: C 46 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7871 (mtp85) REVERT: C 215 GLU cc_start: 0.7849 (pt0) cc_final: 0.7418 (pp20) REVERT: C 217 MET cc_start: 0.8412 (mmm) cc_final: 0.8104 (mmm) REVERT: C 228 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7692 (p0) REVERT: C 247 ASP cc_start: 0.7731 (t0) cc_final: 0.7454 (t0) REVERT: C 260 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: C 286 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8478 (mt) REVERT: D 17 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8794 (mm-30) REVERT: D 20 LYS cc_start: 0.9233 (ttpp) cc_final: 0.8682 (tmtt) REVERT: D 21 MET cc_start: 0.8746 (mmm) cc_final: 0.8426 (mmm) REVERT: D 22 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: D 47 GLU cc_start: 0.8425 (mp0) cc_final: 0.8013 (mp0) REVERT: E 13 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8606 (mm110) REVERT: E 46 GLU cc_start: 0.8464 (tt0) cc_final: 0.8189 (tt0) REVERT: E 65 LYS cc_start: 0.8409 (tttp) cc_final: 0.8050 (ttpt) REVERT: E 151 LYS cc_start: 0.8779 (tttt) cc_final: 0.8554 (ttpt) REVERT: E 222 GLU cc_start: 0.8823 (pt0) cc_final: 0.8579 (pt0) outliers start: 21 outliers final: 12 residues processed: 154 average time/residue: 0.5420 time to fit residues: 88.7505 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083878 restraints weight = 13316.109| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.69 r_work: 0.2870 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8965 Z= 0.131 Angle : 0.573 12.191 12173 Z= 0.288 Chirality : 0.041 0.295 1386 Planarity : 0.003 0.038 1522 Dihedral : 4.847 44.795 1281 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.84 % Allowed : 20.61 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.12 (0.25), residues: 1107 helix: 1.91 (0.26), residues: 397 sheet: 0.43 (0.33), residues: 247 loop : -0.02 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 208 TYR 0.011 0.001 TYR E 178 PHE 0.010 0.001 PHE C 199 TRP 0.023 0.001 TRP A 316 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8962) covalent geometry : angle 0.57271 (12167) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.59773 ( 6) hydrogen bonds : bond 0.03610 ( 456) hydrogen bonds : angle 4.29137 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8022 (t0) cc_final: 0.7748 (t0) REVERT: A 94 ASP cc_start: 0.8708 (t0) cc_final: 0.8388 (t0) REVERT: A 130 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8047 (tm) REVERT: B 9 ASP cc_start: 0.7940 (m-30) cc_final: 0.7456 (m-30) REVERT: B 20 ASP cc_start: 0.7785 (t0) cc_final: 0.7477 (m-30) REVERT: B 24 ARG cc_start: 0.7331 (ttp80) cc_final: 0.7103 (ttm110) REVERT: B 305 CYS cc_start: 0.8296 (m) cc_final: 0.7825 (t) REVERT: C 23 LYS cc_start: 0.9171 (ttmm) cc_final: 0.8760 (ttpp) REVERT: C 46 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7878 (mtp85) REVERT: C 215 GLU cc_start: 0.7910 (pt0) cc_final: 0.7474 (pp20) REVERT: C 217 MET cc_start: 0.8402 (mmm) cc_final: 0.8097 (mmm) REVERT: C 228 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7696 (p0) REVERT: C 247 ASP cc_start: 0.7747 (t0) cc_final: 0.7490 (t0) REVERT: C 286 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8499 (mt) REVERT: D 17 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8765 (mm-30) REVERT: D 20 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8657 (tmtt) REVERT: D 21 MET cc_start: 0.8733 (mmm) cc_final: 0.8412 (mmm) REVERT: D 22 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: D 47 GLU cc_start: 0.8411 (mp0) cc_final: 0.7978 (mp0) REVERT: E 13 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8604 (mm110) REVERT: E 46 GLU cc_start: 0.8462 (tt0) cc_final: 0.8183 (tt0) REVERT: E 65 LYS cc_start: 0.8499 (tttp) cc_final: 0.8156 (ttpt) REVERT: E 151 LYS cc_start: 0.8764 (tttt) cc_final: 0.8536 (ttpt) REVERT: E 222 GLU cc_start: 0.8822 (pt0) cc_final: 0.8564 (pt0) outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 0.5455 time to fit residues: 86.1143 Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 22 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS C 32 GLN C 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083237 restraints weight = 13163.963| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.64 r_work: 0.2869 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8965 Z= 0.143 Angle : 0.565 12.017 12173 Z= 0.285 Chirality : 0.042 0.287 1386 Planarity : 0.003 0.038 1522 Dihedral : 4.858 44.636 1281 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.39 % Allowed : 19.74 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.11 (0.25), residues: 1107 helix: 1.90 (0.26), residues: 397 sheet: 0.40 (0.33), residues: 247 loop : -0.01 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 208 TYR 0.011 0.001 TYR E 178 PHE 0.010 0.001 PHE C 199 TRP 0.025 0.001 TRP A 316 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8962) covalent geometry : angle 0.56498 (12167) SS BOND : bond 0.00162 ( 3) SS BOND : angle 0.67591 ( 6) hydrogen bonds : bond 0.03636 ( 456) hydrogen bonds : angle 4.30823 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2953.55 seconds wall clock time: 51 minutes 13.90 seconds (3073.90 seconds total)