Starting phenix.real_space_refine on Fri Aug 22 21:46:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9s_35282/08_2025/8i9s_35282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9s_35282/08_2025/8i9s_35282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i9s_35282/08_2025/8i9s_35282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9s_35282/08_2025/8i9s_35282.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i9s_35282/08_2025/8i9s_35282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9s_35282/08_2025/8i9s_35282.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 54 5.16 5 C 5183 2.51 5 N 1402 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2046 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1558 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2427 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1689 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 2.23, per 1000 atoms: 0.27 Number of scatterers: 8123 At special positions: 0 Unit cell: (87.4526, 122.235, 124.223, 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 54 16.00 O 1484 8.00 N 1402 7.00 C 5183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 355 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 511.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.826A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 removed outlier: 3.865A pdb=" N ILE C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 3.789A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 5.089A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.887A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 154 removed outlier: 3.665A pdb=" N ALA C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 333 through 363 removed outlier: 5.889A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 373 through 403 removed outlier: 3.723A pdb=" N ARG C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.611A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 436 removed outlier: 6.348A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.083A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.551A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.689A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.536A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.628A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.802A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.856A pdb=" N GLU C 162 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 173 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 164 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 171 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.465A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.664A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.611A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.044A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.059A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.657A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.920A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.709A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.546A pdb=" N MET H 83 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.349A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 39 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.349A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 39 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.573A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.548A pdb=" N VAL H 226 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1173 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: 1.64 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2642 1.34 - 1.46: 2027 1.46 - 1.58: 3558 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8298 Sorted by residual: bond pdb=" C ILE C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 bond pdb=" C LEU C 38 " pdb=" N PRO C 39 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.30e-02 5.92e+03 1.06e+00 bond pdb=" C ILE C 155 " pdb=" N PRO C 156 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.72e-01 bond pdb=" C THR C 391 " pdb=" N PRO C 392 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.32e-01 bond pdb=" CB PRO A 315 " pdb=" CG PRO A 315 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.25e-01 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11049 1.50 - 2.99: 192 2.99 - 4.49: 48 4.49 - 5.99: 10 5.99 - 7.48: 8 Bond angle restraints: 11307 Sorted by residual: angle pdb=" CB MET C 27 " pdb=" CG MET C 27 " pdb=" SD MET C 27 " ideal model delta sigma weight residual 112.70 119.42 -6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" CA LEU A 274 " pdb=" CB LEU A 274 " pdb=" CG LEU A 274 " ideal model delta sigma weight residual 116.30 123.78 -7.48 3.50e+00 8.16e-02 4.57e+00 angle pdb=" C CYS A 325 " pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.55e+00 angle pdb=" CB PRO G 60 " pdb=" CG PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 106.10 99.36 6.74 3.20e+00 9.77e-02 4.44e+00 angle pdb=" C ILE C 98 " pdb=" CA ILE C 98 " pdb=" CB ILE C 98 " ideal model delta sigma weight residual 114.00 111.27 2.73 1.31e+00 5.83e-01 4.33e+00 ... (remaining 11302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4419 16.92 - 33.85: 347 33.85 - 50.77: 68 50.77 - 67.69: 8 67.69 - 84.62: 6 Dihedral angle restraints: 4848 sinusoidal: 1641 harmonic: 3207 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 355 " pdb=" CB CYS C 355 " ideal model delta sinusoidal sigma weight residual 93.00 129.44 -36.44 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N SER C 100 " pdb=" CA SER C 100 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA TYR H 101 " pdb=" C TYR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1099 0.056 - 0.112: 207 0.112 - 0.168: 15 0.168 - 0.224: 0 0.224 - 0.280: 1 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE A 266 " pdb=" N ILE A 266 " pdb=" C ILE A 266 " pdb=" CB ILE A 266 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1319 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 314 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 315 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 20 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 21 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.030 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO G 60 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1794 2.79 - 3.32: 7330 3.32 - 3.84: 12601 3.84 - 4.37: 14066 4.37 - 4.90: 25704 Nonbonded interactions: 61495 Sorted by model distance: nonbonded pdb=" O ALA C 48 " pdb=" NH2 ARG C 54 " model vdw 2.260 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C 55 " pdb=" OD1 ASN C 57 " model vdw 2.265 3.040 nonbonded pdb=" O CYS A 255 " pdb=" NZ LYS A 317 " model vdw 2.288 3.120 nonbonded pdb=" O LEU C 75 " pdb=" OG SER C 78 " model vdw 2.313 3.040 ... (remaining 61490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.002 0.045 8302 Z= 0.113 Angle : 0.560 7.482 11315 Z= 0.290 Chirality : 0.042 0.280 1322 Planarity : 0.005 0.086 1441 Dihedral : 12.767 84.615 2766 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.32 (0.26), residues: 1095 helix: 1.96 (0.28), residues: 367 sheet: -0.25 (0.31), residues: 281 loop : -0.94 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 349 TYR 0.011 0.001 TYR H 101 PHE 0.018 0.001 PHE C 442 TRP 0.012 0.001 TRP A 212 HIS 0.005 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8298) covalent geometry : angle 0.55903 (11307) SS BOND : bond 0.00449 ( 4) SS BOND : angle 1.08568 ( 8) hydrogen bonds : bond 0.17573 ( 404) hydrogen bonds : angle 6.49328 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.331 Fit side-chains REVERT: C 27 MET cc_start: 0.5303 (mpp) cc_final: 0.3484 (tmm) REVERT: C 138 MET cc_start: 0.7544 (mmm) cc_final: 0.7189 (ttm) REVERT: C 414 MET cc_start: 0.4556 (ptt) cc_final: 0.4304 (ptt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0970 time to fit residues: 19.2219 Evaluate side-chains 105 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 HIS C 427 ASN A 270 ASN G 59 ASN H 39 GLN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140190 restraints weight = 10660.514| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.65 r_work: 0.3551 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8302 Z= 0.164 Angle : 0.617 6.836 11315 Z= 0.323 Chirality : 0.045 0.184 1322 Planarity : 0.005 0.051 1441 Dihedral : 4.223 28.269 1182 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.52 % Allowed : 8.59 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.18 (0.26), residues: 1095 helix: 1.76 (0.28), residues: 378 sheet: -0.07 (0.31), residues: 275 loop : -1.20 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.014 0.002 TYR H 190 PHE 0.021 0.002 PHE B 234 TRP 0.020 0.002 TRP B 211 HIS 0.006 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8298) covalent geometry : angle 0.61630 (11307) SS BOND : bond 0.00757 ( 4) SS BOND : angle 1.12849 ( 8) hydrogen bonds : bond 0.04928 ( 404) hydrogen bonds : angle 4.64091 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.321 Fit side-chains REVERT: A 53 MET cc_start: 0.6586 (mtm) cc_final: 0.6290 (mtm) REVERT: A 255 CYS cc_start: 0.7627 (p) cc_final: 0.7357 (p) REVERT: B 154 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7746 (t0) REVERT: H 80 PHE cc_start: 0.7921 (m-80) cc_final: 0.7547 (m-80) outliers start: 12 outliers final: 9 residues processed: 132 average time/residue: 0.0874 time to fit residues: 16.3286 Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.174571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143335 restraints weight = 10582.850| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.00 r_work: 0.3658 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8302 Z= 0.133 Angle : 0.555 5.789 11315 Z= 0.291 Chirality : 0.043 0.230 1322 Planarity : 0.004 0.047 1441 Dihedral : 4.031 28.633 1182 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.52 % Allowed : 11.99 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.22 (0.26), residues: 1095 helix: 1.80 (0.28), residues: 377 sheet: -0.14 (0.31), residues: 289 loop : -1.14 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.013 0.001 PHE A 192 TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8298) covalent geometry : angle 0.55439 (11307) SS BOND : bond 0.00612 ( 4) SS BOND : angle 1.09508 ( 8) hydrogen bonds : bond 0.04441 ( 404) hydrogen bonds : angle 4.35899 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.309 Fit side-chains REVERT: A 24 LYS cc_start: 0.8437 (ttpp) cc_final: 0.8165 (tttp) REVERT: A 208 GLU cc_start: 0.7072 (tp30) cc_final: 0.6559 (mt-10) REVERT: A 255 CYS cc_start: 0.7547 (p) cc_final: 0.7184 (p) REVERT: A 309 GLU cc_start: 0.6450 (tt0) cc_final: 0.6021 (tm-30) REVERT: B 154 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7849 (t0) REVERT: H 80 PHE cc_start: 0.7985 (m-80) cc_final: 0.7692 (m-80) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 0.0742 time to fit residues: 13.9852 Evaluate side-chains 117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.173910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.142573 restraints weight = 10850.578| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.19 r_work: 0.3643 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8302 Z= 0.124 Angle : 0.538 5.727 11315 Z= 0.281 Chirality : 0.043 0.257 1322 Planarity : 0.004 0.048 1441 Dihedral : 3.958 27.904 1182 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.64 % Allowed : 13.51 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.36 (0.26), residues: 1095 helix: 2.02 (0.29), residues: 371 sheet: -0.15 (0.30), residues: 296 loop : -1.05 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.013 0.001 PHE B 241 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8298) covalent geometry : angle 0.53702 (11307) SS BOND : bond 0.00623 ( 4) SS BOND : angle 1.29236 ( 8) hydrogen bonds : bond 0.04078 ( 404) hydrogen bonds : angle 4.24762 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.321 Fit side-chains REVERT: A 24 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8236 (tttp) REVERT: A 208 GLU cc_start: 0.7109 (tp30) cc_final: 0.6569 (mt-10) REVERT: A 255 CYS cc_start: 0.7463 (p) cc_final: 0.7214 (p) REVERT: A 309 GLU cc_start: 0.6465 (tt0) cc_final: 0.6040 (tm-30) REVERT: B 154 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7895 (t0) REVERT: B 214 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7576 (mmt-90) REVERT: H 80 PHE cc_start: 0.8011 (m-80) cc_final: 0.7780 (m-80) REVERT: H 140 MET cc_start: 0.7847 (mtp) cc_final: 0.7408 (ttt) outliers start: 13 outliers final: 9 residues processed: 134 average time/residue: 0.0761 time to fit residues: 15.0499 Evaluate side-chains 121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137605 restraints weight = 10665.887| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.72 r_work: 0.3520 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8302 Z= 0.127 Angle : 0.534 5.605 11315 Z= 0.279 Chirality : 0.043 0.254 1322 Planarity : 0.004 0.049 1441 Dihedral : 3.919 27.409 1182 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.35 (0.26), residues: 1095 helix: 2.05 (0.29), residues: 370 sheet: -0.15 (0.30), residues: 297 loop : -1.10 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 161 TYR 0.012 0.001 TYR H 190 PHE 0.014 0.001 PHE B 241 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8298) covalent geometry : angle 0.53280 (11307) SS BOND : bond 0.00632 ( 4) SS BOND : angle 1.27526 ( 8) hydrogen bonds : bond 0.04175 ( 404) hydrogen bonds : angle 4.18705 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.324 Fit side-chains REVERT: A 24 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8260 (tttp) REVERT: A 208 GLU cc_start: 0.7068 (tp30) cc_final: 0.6634 (mt-10) REVERT: A 255 CYS cc_start: 0.7516 (p) cc_final: 0.7202 (p) REVERT: A 309 GLU cc_start: 0.6319 (tt0) cc_final: 0.5997 (tm-30) REVERT: B 45 MET cc_start: 0.8857 (mmm) cc_final: 0.8328 (mtt) REVERT: B 154 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7876 (t0) REVERT: B 214 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7562 (mmt-90) REVERT: G 21 MET cc_start: 0.7900 (ttp) cc_final: 0.7597 (tmm) REVERT: H 115 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7560 (t) outliers start: 16 outliers final: 10 residues processed: 135 average time/residue: 0.0807 time to fit residues: 15.9083 Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.167063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137559 restraints weight = 10620.952| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.70 r_work: 0.3521 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8302 Z= 0.124 Angle : 0.540 7.049 11315 Z= 0.281 Chirality : 0.043 0.287 1322 Planarity : 0.004 0.051 1441 Dihedral : 3.937 29.033 1182 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.53 % Allowed : 14.90 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.38 (0.26), residues: 1095 helix: 2.03 (0.28), residues: 370 sheet: 0.02 (0.31), residues: 287 loop : -1.14 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8298) covalent geometry : angle 0.53940 (11307) SS BOND : bond 0.00643 ( 4) SS BOND : angle 1.23395 ( 8) hydrogen bonds : bond 0.04064 ( 404) hydrogen bonds : angle 4.12620 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.335 Fit side-chains REVERT: A 24 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8259 (tttp) REVERT: A 208 GLU cc_start: 0.7018 (tp30) cc_final: 0.6601 (mt-10) REVERT: A 255 CYS cc_start: 0.7466 (p) cc_final: 0.7168 (p) REVERT: A 309 GLU cc_start: 0.6307 (tt0) cc_final: 0.5982 (tm-30) REVERT: B 45 MET cc_start: 0.8865 (mmm) cc_final: 0.8382 (mtt) REVERT: B 154 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7910 (t0) REVERT: B 175 GLN cc_start: 0.8158 (mm110) cc_final: 0.7734 (mm-40) REVERT: B 214 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7522 (mmt-90) REVERT: G 21 MET cc_start: 0.7840 (ttp) cc_final: 0.7551 (tmm) REVERT: H 80 PHE cc_start: 0.7968 (m-80) cc_final: 0.7720 (m-80) REVERT: H 115 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7536 (t) outliers start: 20 outliers final: 13 residues processed: 131 average time/residue: 0.0858 time to fit residues: 16.1481 Evaluate side-chains 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 0.0060 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138632 restraints weight = 10662.689| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.68 r_work: 0.3532 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8302 Z= 0.115 Angle : 0.522 6.677 11315 Z= 0.272 Chirality : 0.043 0.288 1322 Planarity : 0.004 0.051 1441 Dihedral : 3.852 28.536 1182 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.02 % Allowed : 15.66 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.47 (0.26), residues: 1095 helix: 2.09 (0.29), residues: 370 sheet: 0.15 (0.31), residues: 281 loop : -1.12 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8298) covalent geometry : angle 0.52112 (11307) SS BOND : bond 0.00625 ( 4) SS BOND : angle 1.21342 ( 8) hydrogen bonds : bond 0.03870 ( 404) hydrogen bonds : angle 4.04618 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.313 Fit side-chains REVERT: A 24 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8206 (tttp) REVERT: A 208 GLU cc_start: 0.6973 (tp30) cc_final: 0.6594 (mt-10) REVERT: A 250 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 255 CYS cc_start: 0.7407 (p) cc_final: 0.7122 (p) REVERT: A 309 GLU cc_start: 0.6295 (tt0) cc_final: 0.5995 (tm-30) REVERT: B 45 MET cc_start: 0.8880 (mmm) cc_final: 0.8392 (mtt) REVERT: B 154 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7868 (t0) REVERT: B 175 GLN cc_start: 0.8175 (mm110) cc_final: 0.7765 (mm110) REVERT: B 214 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7534 (mmt-90) REVERT: G 21 MET cc_start: 0.7787 (ttp) cc_final: 0.7554 (tmm) outliers start: 16 outliers final: 12 residues processed: 133 average time/residue: 0.0854 time to fit residues: 16.2650 Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 0.0020 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140653 restraints weight = 10571.045| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.70 r_work: 0.3544 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8302 Z= 0.103 Angle : 0.507 6.513 11315 Z= 0.263 Chirality : 0.043 0.318 1322 Planarity : 0.004 0.052 1441 Dihedral : 3.721 27.222 1182 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.78 % Allowed : 15.53 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.58 (0.27), residues: 1095 helix: 2.15 (0.28), residues: 370 sheet: 0.29 (0.31), residues: 280 loop : -1.09 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.011 0.001 TYR H 190 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8298) covalent geometry : angle 0.50636 (11307) SS BOND : bond 0.00531 ( 4) SS BOND : angle 1.08207 ( 8) hydrogen bonds : bond 0.03503 ( 404) hydrogen bonds : angle 3.95482 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.317 Fit side-chains REVERT: A 24 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8215 (tttp) REVERT: A 208 GLU cc_start: 0.6985 (tp30) cc_final: 0.6605 (mt-10) REVERT: A 250 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 255 CYS cc_start: 0.7359 (p) cc_final: 0.7114 (p) REVERT: A 309 GLU cc_start: 0.6287 (tt0) cc_final: 0.6069 (tm-30) REVERT: B 45 MET cc_start: 0.8853 (mmm) cc_final: 0.8331 (mtt) REVERT: B 154 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7900 (t0) REVERT: B 175 GLN cc_start: 0.8179 (mm110) cc_final: 0.7777 (mm110) REVERT: B 214 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7565 (mmt-90) REVERT: G 21 MET cc_start: 0.7773 (ttp) cc_final: 0.7564 (tmm) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.0860 time to fit residues: 16.4548 Evaluate side-chains 132 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 0.0050 chunk 85 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138225 restraints weight = 10636.545| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.60 r_work: 0.3523 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8302 Z= 0.129 Angle : 0.551 9.439 11315 Z= 0.284 Chirality : 0.044 0.324 1322 Planarity : 0.004 0.053 1441 Dihedral : 3.878 28.706 1182 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.65 % Allowed : 15.78 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.53 (0.27), residues: 1095 helix: 2.12 (0.28), residues: 370 sheet: 0.19 (0.31), residues: 286 loop : -1.09 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.013 0.001 PHE B 241 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8298) covalent geometry : angle 0.55015 (11307) SS BOND : bond 0.00670 ( 4) SS BOND : angle 1.25498 ( 8) hydrogen bonds : bond 0.04114 ( 404) hydrogen bonds : angle 4.02971 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.283 Fit side-chains REVERT: A 24 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8287 (tttp) REVERT: A 208 GLU cc_start: 0.7007 (tp30) cc_final: 0.6675 (mt-10) REVERT: A 250 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8323 (tt) REVERT: A 255 CYS cc_start: 0.7442 (p) cc_final: 0.7160 (p) REVERT: B 45 MET cc_start: 0.8862 (mmm) cc_final: 0.8404 (mtt) REVERT: B 154 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7877 (t0) REVERT: B 175 GLN cc_start: 0.8219 (mm110) cc_final: 0.7818 (mm110) REVERT: B 214 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7573 (mmt-90) outliers start: 21 outliers final: 14 residues processed: 134 average time/residue: 0.0886 time to fit residues: 16.7506 Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139115 restraints weight = 10720.924| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.73 r_work: 0.3531 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8302 Z= 0.118 Angle : 0.535 6.810 11315 Z= 0.278 Chirality : 0.044 0.349 1322 Planarity : 0.004 0.054 1441 Dihedral : 3.867 28.338 1182 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.15 % Allowed : 16.04 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.55 (0.26), residues: 1095 helix: 2.12 (0.28), residues: 370 sheet: 0.32 (0.31), residues: 280 loop : -1.14 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.013 0.001 PHE B 241 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8298) covalent geometry : angle 0.53408 (11307) SS BOND : bond 0.00644 ( 4) SS BOND : angle 1.23266 ( 8) hydrogen bonds : bond 0.03897 ( 404) hydrogen bonds : angle 4.01363 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.332 Fit side-chains REVERT: A 24 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8265 (tttp) REVERT: A 208 GLU cc_start: 0.6992 (tp30) cc_final: 0.6640 (mt-10) REVERT: A 250 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 255 CYS cc_start: 0.7389 (p) cc_final: 0.7112 (p) REVERT: B 45 MET cc_start: 0.8846 (mmm) cc_final: 0.8416 (mtt) REVERT: B 154 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7877 (t0) REVERT: B 175 GLN cc_start: 0.8204 (mm110) cc_final: 0.7807 (mm110) REVERT: B 214 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7564 (mmt-90) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 0.0879 time to fit residues: 15.7789 Evaluate side-chains 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 36 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140559 restraints weight = 10660.732| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.69 r_work: 0.3543 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8302 Z= 0.106 Angle : 0.521 6.670 11315 Z= 0.270 Chirality : 0.043 0.325 1322 Planarity : 0.004 0.054 1441 Dihedral : 3.751 27.102 1182 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.15 % Allowed : 16.54 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 aren not related in a simple way. whole: 0.62 (0.27), residues: 1095 helix: 2.18 (0.28), residues: 370 sheet: 0.23 (0.31), residues: 291 loop : -1.03 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.012 0.001 TYR H 190 PHE 0.012 0.001 PHE B 241 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.000 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8298) covalent geometry : angle 0.52084 (11307) SS BOND : bond 0.00554 ( 4) SS BOND : angle 1.10811 ( 8) hydrogen bonds : bond 0.03585 ( 404) hydrogen bonds : angle 3.94137 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.50 seconds wall clock time: 45 minutes 35.86 seconds (2735.86 seconds total)