Starting phenix.real_space_refine on Sat Aug 23 12:31:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5m_39775/08_2025/8z5m_39775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5m_39775/08_2025/8z5m_39775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z5m_39775/08_2025/8z5m_39775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5m_39775/08_2025/8z5m_39775.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5m_39775/08_2025/8z5m_39775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5m_39775/08_2025/8z5m_39775.cif" } resolution = 3.66 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 71 atoms to isotropic. 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 70 5.16 5 C 7637 2.51 5 N 2030 2.21 5 O 2269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12006 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7852 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 951} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3057 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 356} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1097 Classifications: {'peptide': 144} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 2.10, per 1000 atoms: 0.17 Number of scatterers: 12006 At special positions: 0 Unit cell: (100.1, 116.6, 144.1, 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 70 16.00 O 2269 8.00 N 2030 7.00 C 7637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 401.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 11 sheets defined 58.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 23 through 26 removed outlier: 3.505A pdb=" N GLN A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.616A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 removed outlier: 3.667A pdb=" N CYS A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.546A pdb=" N VAL A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 removed outlier: 4.022A pdb=" N THR A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 removed outlier: 3.699A pdb=" N ASN A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.689A pdb=" N LYS A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.902A pdb=" N VAL A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.686A pdb=" N LYS A 221 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY A 222 " --> pdb=" O GLY A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.967A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 removed outlier: 3.988A pdb=" N VAL A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 removed outlier: 3.648A pdb=" N PHE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 336 " --> pdb=" O TRP A 332 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.640A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.520A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 416 removed outlier: 3.628A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 4.095A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.087A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.511A pdb=" N THR A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.904A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 526 " --> pdb=" O GLN A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 526' Processing helix chain 'A' and resid 531 through 534 Processing helix chain 'A' and resid 535 through 553 removed outlier: 3.547A pdb=" N ARG A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 603 through 610 removed outlier: 4.193A pdb=" N THR A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 775 through 790 Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.616A pdb=" N TYR A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 removed outlier: 3.548A pdb=" N ILE A 832 " --> pdb=" O TYR A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 850 removed outlier: 3.793A pdb=" N HIS A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 888 through 908 removed outlier: 3.659A pdb=" N ILE A 892 " --> pdb=" O MET A 888 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 907 " --> pdb=" O MET A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 936 Processing helix chain 'A' and resid 938 through 948 Processing helix chain 'A' and resid 950 through 964 Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1095 through 1100 removed outlier: 3.766A pdb=" N GLU A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 4.090A pdb=" N SER A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1141 removed outlier: 3.769A pdb=" N ASP A1139 " --> pdb=" O THR A1135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A1140 " --> pdb=" O MET A1136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A1141 " --> pdb=" O LEU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1170 Processing helix chain 'A' and resid 1185 through 1191 removed outlier: 3.874A pdb=" N TYR A1189 " --> pdb=" O CYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1214 removed outlier: 3.928A pdb=" N TYR A1202 " --> pdb=" O GLY A1198 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1214 " --> pdb=" O TYR A1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 removed outlier: 4.111A pdb=" N PHE C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 60 through 82 removed outlier: 3.889A pdb=" N LYS C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.915A pdb=" N TYR C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 144 removed outlier: 3.799A pdb=" N LYS C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.516A pdb=" N ASP C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.681A pdb=" N LYS C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 300 through 324 removed outlier: 4.120A pdb=" N TYR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'D' and resid 6 through 21 Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.569A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.533A pdb=" N ILE A 360 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.998A pdb=" N LEU A 372 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 562 through 563 removed outlier: 6.578A pdb=" N VAL A 440 " --> pdb=" O GLN A 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.441A pdb=" N ARG A 472 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 511 " --> pdb=" O PHE A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.511A pdb=" N PHE A1090 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1092 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1085 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY A1084 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 20 through 28 removed outlier: 5.948A pdb=" N ILE C 38 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU C 24 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 34 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG C 28 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 33 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL C 50 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU C 95 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 101 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 93 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 103 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.746A pdb=" N VAL C 147 " --> pdb=" O CYS C 173 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 173 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 156 through 158 removed outlier: 3.637A pdb=" N LEU C 157 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 165 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 556 hydrogen bonds defined for protein. 1611 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: 1.84 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2047 1.32 - 1.44: 3126 1.44 - 1.56: 6956 1.56 - 1.69: 1 1.69 - 1.81: 119 Bond restraints: 12249 Sorted by residual: bond pdb=" N LYS C 209 " pdb=" CA LYS C 209 " ideal model delta sigma weight residual 1.458 1.373 0.085 1.27e-02 6.20e+03 4.51e+01 bond pdb=" CA THR C 54 " pdb=" C THR C 54 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.25e-02 6.40e+03 3.10e+01 bond pdb=" CA VAL C 53 " pdb=" C VAL C 53 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.27e-02 6.20e+03 2.57e+01 bond pdb=" CA PHE C 16 " pdb=" C PHE C 16 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.26e-02 6.30e+03 2.38e+01 bond pdb=" C LYS A1077 " pdb=" O LYS A1077 " ideal model delta sigma weight residual 1.236 1.192 0.045 1.15e-02 7.56e+03 1.52e+01 ... (remaining 12244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 16549 5.21 - 10.43: 30 10.43 - 15.64: 3 15.64 - 20.85: 1 20.85 - 26.07: 1 Bond angle restraints: 16584 Sorted by residual: angle pdb=" C ILE C 88 " pdb=" N GLN C 89 " pdb=" CA GLN C 89 " ideal model delta sigma weight residual 123.05 111.44 11.61 1.40e+00 5.10e-01 6.88e+01 angle pdb=" CD LYS A 836 " pdb=" CE LYS A 836 " pdb=" NZ LYS A 836 " ideal model delta sigma weight residual 111.90 137.97 -26.07 3.20e+00 9.77e-02 6.63e+01 angle pdb=" C LYS C 108 " pdb=" CA LYS C 108 " pdb=" CB LYS C 108 " ideal model delta sigma weight residual 110.42 94.29 16.13 1.99e+00 2.53e-01 6.57e+01 angle pdb=" N LEU A1079 " pdb=" CA LEU A1079 " pdb=" C LEU A1079 " ideal model delta sigma weight residual 111.71 103.13 8.58 1.15e+00 7.56e-01 5.57e+01 angle pdb=" N THR C 54 " pdb=" CA THR C 54 " pdb=" C THR C 54 " ideal model delta sigma weight residual 114.09 103.09 11.00 1.55e+00 4.16e-01 5.03e+01 ... (remaining 16579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6290 17.94 - 35.89: 794 35.89 - 53.83: 266 53.83 - 71.78: 50 71.78 - 89.72: 19 Dihedral angle restraints: 7419 sinusoidal: 3008 harmonic: 4411 Sorted by residual: dihedral pdb=" C LYS C 108 " pdb=" N LYS C 108 " pdb=" CA LYS C 108 " pdb=" CB LYS C 108 " ideal model delta harmonic sigma weight residual -122.60 -104.17 -18.43 0 2.50e+00 1.60e-01 5.43e+01 dihedral pdb=" CA PHE C 99 " pdb=" C PHE C 99 " pdb=" N PHE C 100 " pdb=" CA PHE C 100 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N PRO A 399 " pdb=" CA PRO A 399 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 7416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1745 0.077 - 0.154: 110 0.154 - 0.231: 7 0.231 - 0.308: 2 0.308 - 0.385: 2 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CA THR C 42 " pdb=" N THR C 42 " pdb=" C THR C 42 " pdb=" CB THR C 42 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA LYS C 108 " pdb=" N LYS C 108 " pdb=" C LYS C 108 " pdb=" CB LYS C 108 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB THR C 42 " pdb=" CA THR C 42 " pdb=" OG1 THR C 42 " pdb=" CG2 THR C 42 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1863 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 94 " -0.052 2.00e-02 2.50e+03 3.27e-02 2.13e+01 pdb=" CG TYR C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR C 94 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 94 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 94 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 94 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR C 94 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 94 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 207 " 0.020 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C TYR C 207 " -0.065 2.00e-02 2.50e+03 pdb=" O TYR C 207 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY C 208 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 52 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASP C 52 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 52 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL C 53 " -0.022 2.00e-02 2.50e+03 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 159 2.61 - 3.18: 10657 3.18 - 3.75: 17403 3.75 - 4.33: 21975 4.33 - 4.90: 38224 Nonbonded interactions: 88418 Sorted by model distance: nonbonded pdb=" O LYS C 40 " pdb=" N THR C 42 " model vdw 2.032 3.120 nonbonded pdb=" O LEU A 260 " pdb=" OG SER A 264 " model vdw 2.124 3.040 nonbonded pdb=" O VAL A 837 " pdb=" OH TYR A 873 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASN D 61 " pdb=" OG1 THR D 63 " model vdw 2.178 3.040 nonbonded pdb=" OE2 GLU A1129 " pdb=" OH TYR C 355 " model vdw 2.180 3.040 ... (remaining 88413 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 group one per residue 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: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.090 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 12249 Z= 0.255 Angle : 0.647 26.066 16584 Z= 0.371 Chirality : 0.040 0.385 1866 Planarity : 0.004 0.053 2135 Dihedral : 18.280 89.722 4577 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.64 % Favored : 93.09 % Rotamer: Outliers : 1.07 % Allowed : 23.09 % Favored : 75.84 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.12 % 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: 2.00 (0.24), residues: 1505 helix: 3.49 (0.20), residues: 743 sheet: 0.56 (0.61), residues: 67 loop : -1.15 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.054 0.001 TYR C 94 PHE 0.028 0.001 PHE C 99 TRP 0.006 0.001 TRP C 358 HIS 0.001 0.000 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00394 (12249) covalent geometry : angle 0.64688 (16584) hydrogen bonds : bond 0.15962 ( 556) hydrogen bonds : angle 4.67160 ( 1611) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8996 (mm) cc_final: 0.8770 (mp) REVERT: A 781 ASP cc_start: 0.6443 (t70) cc_final: 0.6136 (t70) REVERT: A 1123 TYR cc_start: 0.7197 (m-80) cc_final: 0.6159 (m-80) REVERT: C 165 LYS cc_start: 0.8043 (ptpt) cc_final: 0.7691 (mttp) outliers start: 14 outliers final: 6 residues processed: 204 average time/residue: 0.0860 time to fit residues: 25.9072 Evaluate side-chains 167 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 147 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.0270 chunk 149 optimal weight: 6.9990 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 HIS ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140853 restraints weight = 19352.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141902 restraints weight = 14883.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142821 restraints weight = 12303.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143675 restraints weight = 10937.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143971 restraints weight = 9993.220| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12249 Z= 0.109 Angle : 0.528 7.615 16584 Z= 0.273 Chirality : 0.039 0.186 1866 Planarity : 0.004 0.040 2135 Dihedral : 4.408 51.919 1660 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 2.82 % Allowed : 21.72 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.67 (0.23), residues: 1505 helix: 3.02 (0.19), residues: 758 sheet: 1.00 (0.60), residues: 67 loop : -1.23 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 107 TYR 0.009 0.001 TYR C 320 PHE 0.011 0.001 PHE C 16 TRP 0.008 0.001 TRP C 358 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00224 (12249) covalent geometry : angle 0.52758 (16584) hydrogen bonds : bond 0.03517 ( 556) hydrogen bonds : angle 3.65718 ( 1611) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7504 (tp) cc_final: 0.7252 (tt) REVERT: A 781 ASP cc_start: 0.6573 (t70) cc_final: 0.6274 (t70) REVERT: A 1123 TYR cc_start: 0.7204 (m-80) cc_final: 0.6100 (m-80) REVERT: C 220 MET cc_start: 0.8341 (ttt) cc_final: 0.7929 (ttt) REVERT: C 363 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7176 (tm-30) REVERT: C 379 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6478 (tp) REVERT: D 81 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6885 (t0) outliers start: 37 outliers final: 22 residues processed: 199 average time/residue: 0.0867 time to fit residues: 26.1229 Evaluate side-chains 181 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.163943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138932 restraints weight = 19631.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139014 restraints weight = 17611.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139241 restraints weight = 15887.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139358 restraints weight = 15131.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139480 restraints weight = 14465.388| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12249 Z= 0.113 Angle : 0.517 7.606 16584 Z= 0.266 Chirality : 0.038 0.133 1866 Planarity : 0.004 0.045 2135 Dihedral : 3.561 35.971 1652 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 3.20 % Allowed : 21.88 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.50 (0.23), residues: 1505 helix: 2.82 (0.19), residues: 767 sheet: 0.95 (0.62), residues: 67 loop : -1.30 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 936 TYR 0.011 0.001 TYR C 320 PHE 0.007 0.001 PHE C 59 TRP 0.010 0.001 TRP C 358 HIS 0.003 0.001 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00248 (12249) covalent geometry : angle 0.51734 (16584) hydrogen bonds : bond 0.03889 ( 556) hydrogen bonds : angle 3.49357 ( 1611) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8401 (mmtt) REVERT: A 1123 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: C 220 MET cc_start: 0.8445 (ttt) cc_final: 0.8144 (ttt) REVERT: C 379 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6393 (tp) REVERT: D 81 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6971 (t0) outliers start: 42 outliers final: 23 residues processed: 196 average time/residue: 0.0857 time to fit residues: 25.2697 Evaluate side-chains 183 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 121 optimal weight: 0.0010 chunk 138 optimal weight: 3.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137795 restraints weight = 19466.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137578 restraints weight = 17037.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137989 restraints weight = 15834.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138058 restraints weight = 14636.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139013 restraints weight = 13922.449| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12249 Z= 0.111 Angle : 0.523 7.873 16584 Z= 0.268 Chirality : 0.039 0.141 1866 Planarity : 0.004 0.046 2135 Dihedral : 3.546 24.374 1650 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.36 % Rotamer: Outliers : 3.20 % Allowed : 22.64 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.33 (0.23), residues: 1505 helix: 2.70 (0.19), residues: 768 sheet: 0.75 (0.61), residues: 66 loop : -1.40 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.011 0.001 TYR C 320 PHE 0.010 0.001 PHE A 268 TRP 0.007 0.001 TRP A 823 HIS 0.007 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00247 (12249) covalent geometry : angle 0.52349 (16584) hydrogen bonds : bond 0.03804 ( 556) hydrogen bonds : angle 3.43000 ( 1611) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8198 (pp) REVERT: A 424 ASP cc_start: 0.8712 (p0) cc_final: 0.8293 (p0) REVERT: A 617 SER cc_start: 0.8762 (m) cc_final: 0.8257 (t) REVERT: A 1123 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: C 165 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7600 (mttp) REVERT: C 220 MET cc_start: 0.8419 (ttt) cc_final: 0.8125 (ttt) REVERT: C 379 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6385 (tp) outliers start: 42 outliers final: 24 residues processed: 179 average time/residue: 0.0884 time to fit residues: 23.8442 Evaluate side-chains 174 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 123 optimal weight: 0.0040 chunk 108 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 100 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.162595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138602 restraints weight = 19565.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137983 restraints weight = 18659.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139160 restraints weight = 17383.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139587 restraints weight = 14232.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139684 restraints weight = 12865.200| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12249 Z= 0.103 Angle : 0.507 7.485 16584 Z= 0.261 Chirality : 0.038 0.128 1866 Planarity : 0.004 0.046 2135 Dihedral : 3.490 24.109 1649 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 3.58 % Allowed : 22.10 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.33 (0.23), residues: 1505 helix: 2.69 (0.19), residues: 770 sheet: 0.82 (0.62), residues: 66 loop : -1.42 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.012 0.001 TYR C 319 PHE 0.008 0.001 PHE A 268 TRP 0.007 0.001 TRP A 554 HIS 0.003 0.000 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00226 (12249) covalent geometry : angle 0.50724 (16584) hydrogen bonds : bond 0.03516 ( 556) hydrogen bonds : angle 3.35819 ( 1611) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.5787 (t80) REVERT: A 372 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8171 (pp) REVERT: A 424 ASP cc_start: 0.8685 (p0) cc_final: 0.8266 (p0) REVERT: A 617 SER cc_start: 0.8737 (m) cc_final: 0.8278 (t) REVERT: A 1123 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: C 164 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 220 MET cc_start: 0.8450 (ttt) cc_final: 0.8224 (ttt) REVERT: D 93 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7469 (t80) outliers start: 47 outliers final: 30 residues processed: 189 average time/residue: 0.0827 time to fit residues: 23.9699 Evaluate side-chains 179 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 146 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 37 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.160698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136771 restraints weight = 19599.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136353 restraints weight = 18178.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137554 restraints weight = 17656.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137787 restraints weight = 14948.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137894 restraints weight = 13684.259| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12249 Z= 0.117 Angle : 0.526 7.385 16584 Z= 0.271 Chirality : 0.038 0.129 1866 Planarity : 0.004 0.045 2135 Dihedral : 3.584 24.944 1649 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 3.35 % Allowed : 23.40 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.23), residues: 1505 helix: 2.65 (0.19), residues: 770 sheet: 0.70 (0.64), residues: 66 loop : -1.48 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.013 0.001 TYR C 319 PHE 0.009 0.001 PHE A 268 TRP 0.007 0.001 TRP A 823 HIS 0.002 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00263 (12249) covalent geometry : angle 0.52564 (16584) hydrogen bonds : bond 0.03924 ( 556) hydrogen bonds : angle 3.39609 ( 1611) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.5855 (t80) REVERT: A 372 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8201 (pp) REVERT: A 398 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6573 (pp) REVERT: A 424 ASP cc_start: 0.8674 (p0) cc_final: 0.8316 (p0) REVERT: A 617 SER cc_start: 0.8735 (m) cc_final: 0.8295 (t) REVERT: A 1123 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: C 165 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7662 (mttp) REVERT: C 379 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6536 (tp) REVERT: D 93 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7489 (t80) outliers start: 44 outliers final: 30 residues processed: 184 average time/residue: 0.0971 time to fit residues: 26.8057 Evaluate side-chains 180 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 149 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.158801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132212 restraints weight = 19477.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131839 restraints weight = 17322.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133326 restraints weight = 14130.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133935 restraints weight = 11791.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134262 restraints weight = 10584.317| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12249 Z= 0.125 Angle : 0.546 8.686 16584 Z= 0.280 Chirality : 0.039 0.128 1866 Planarity : 0.004 0.045 2135 Dihedral : 3.704 26.268 1649 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.56 % Rotamer: Outliers : 3.73 % Allowed : 23.25 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.10 (0.23), residues: 1505 helix: 2.58 (0.20), residues: 767 sheet: 0.57 (0.67), residues: 61 loop : -1.58 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.013 0.001 TYR C 319 PHE 0.010 0.001 PHE A 144 TRP 0.008 0.001 TRP A 823 HIS 0.002 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00286 (12249) covalent geometry : angle 0.54602 (16584) hydrogen bonds : bond 0.04282 ( 556) hydrogen bonds : angle 3.46845 ( 1611) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6078 (t80) REVERT: A 372 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 398 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6583 (pp) REVERT: A 617 SER cc_start: 0.9043 (m) cc_final: 0.8544 (t) REVERT: A 814 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: A 1123 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: A 1167 LYS cc_start: 0.7219 (tmtt) cc_final: 0.6969 (tmtt) REVERT: C 165 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7545 (mttp) REVERT: C 379 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6826 (tp) REVERT: D 93 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7495 (t80) REVERT: D 116 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6229 (mmmm) outliers start: 49 outliers final: 33 residues processed: 184 average time/residue: 0.1016 time to fit residues: 28.4584 Evaluate side-chains 182 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 814 TYR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.157368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132988 restraints weight = 19305.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132523 restraints weight = 18506.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133155 restraints weight = 16752.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133554 restraints weight = 14849.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133664 restraints weight = 13964.041| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12249 Z= 0.137 Angle : 0.562 7.796 16584 Z= 0.291 Chirality : 0.039 0.126 1866 Planarity : 0.004 0.046 2135 Dihedral : 3.846 28.525 1649 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.77 % Favored : 92.09 % Rotamer: Outliers : 3.73 % Allowed : 23.17 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.96 (0.23), residues: 1505 helix: 2.43 (0.20), residues: 774 sheet: 0.31 (0.68), residues: 61 loop : -1.63 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.012 0.001 TYR C 319 PHE 0.010 0.001 PHE A 144 TRP 0.007 0.001 TRP A 823 HIS 0.002 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00315 (12249) covalent geometry : angle 0.56224 (16584) hydrogen bonds : bond 0.04551 ( 556) hydrogen bonds : angle 3.52852 ( 1611) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6330 (t80) REVERT: A 372 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8268 (pp) REVERT: A 398 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6475 (pp) REVERT: A 617 SER cc_start: 0.8922 (m) cc_final: 0.8457 (t) REVERT: A 814 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: A 1123 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: A 1167 LYS cc_start: 0.7297 (tmtt) cc_final: 0.7075 (tmtt) REVERT: C 165 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7735 (mttp) REVERT: C 379 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6919 (tp) REVERT: D 93 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7432 (t80) REVERT: D 116 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6089 (mmmm) outliers start: 49 outliers final: 37 residues processed: 175 average time/residue: 0.1085 time to fit residues: 28.5830 Evaluate side-chains 176 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 814 TYR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 146 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136580 restraints weight = 19193.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135629 restraints weight = 16738.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135908 restraints weight = 16455.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136336 restraints weight = 15582.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136532 restraints weight = 13967.708| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12249 Z= 0.104 Angle : 0.542 8.614 16584 Z= 0.278 Chirality : 0.038 0.128 1866 Planarity : 0.004 0.046 2135 Dihedral : 3.708 26.537 1649 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.04 % Favored : 92.76 % Rotamer: Outliers : 3.66 % Allowed : 23.63 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.05 (0.23), residues: 1505 helix: 2.51 (0.20), residues: 768 sheet: 0.44 (0.68), residues: 61 loop : -1.56 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.011 0.001 TYR C 319 PHE 0.009 0.001 PHE C 230 TRP 0.010 0.001 TRP A 554 HIS 0.003 0.000 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00221 (12249) covalent geometry : angle 0.54217 (16584) hydrogen bonds : bond 0.03490 ( 556) hydrogen bonds : angle 3.37847 ( 1611) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.484 Fit side-chains REVERT: A 372 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 398 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6557 (pp) REVERT: A 530 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 617 SER cc_start: 0.8793 (m) cc_final: 0.8347 (t) REVERT: A 814 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5724 (m-80) REVERT: A 904 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7244 (t80) REVERT: A 1123 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: C 165 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7703 (mttp) REVERT: C 379 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6835 (tp) REVERT: D 93 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7441 (t80) REVERT: D 116 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6201 (mmmm) outliers start: 48 outliers final: 28 residues processed: 170 average time/residue: 0.0952 time to fit residues: 24.8265 Evaluate side-chains 169 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 814 TYR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.158608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134690 restraints weight = 19396.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133156 restraints weight = 18058.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133748 restraints weight = 17222.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134151 restraints weight = 15449.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134242 restraints weight = 14574.102| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12249 Z= 0.124 Angle : 0.580 13.986 16584 Z= 0.295 Chirality : 0.039 0.127 1866 Planarity : 0.004 0.044 2135 Dihedral : 3.728 27.637 1649 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.71 % Favored : 92.09 % Rotamer: Outliers : 2.97 % Allowed : 23.93 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.96 (0.23), residues: 1505 helix: 2.41 (0.20), residues: 774 sheet: 0.32 (0.68), residues: 61 loop : -1.59 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.013 0.001 TYR C 319 PHE 0.008 0.001 PHE A 268 TRP 0.006 0.001 TRP A 328 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00280 (12249) covalent geometry : angle 0.58048 (16584) hydrogen bonds : bond 0.04062 ( 556) hydrogen bonds : angle 3.46248 ( 1611) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.461 Fit side-chains REVERT: A 341 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6344 (t80) REVERT: A 372 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8266 (pp) REVERT: A 398 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6591 (pp) REVERT: A 530 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: A 617 SER cc_start: 0.8818 (m) cc_final: 0.8364 (t) REVERT: A 814 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5789 (m-80) REVERT: A 904 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7216 (t80) REVERT: A 1123 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: C 165 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7811 (mttp) REVERT: C 379 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6954 (tp) REVERT: D 93 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7410 (t80) REVERT: D 116 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6211 (mmmm) outliers start: 39 outliers final: 26 residues processed: 165 average time/residue: 0.0890 time to fit residues: 22.8528 Evaluate side-chains 171 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 814 TYR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1122 GLU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133098 restraints weight = 19280.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131916 restraints weight = 17383.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132574 restraints weight = 16902.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132657 restraints weight = 15460.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132826 restraints weight = 14425.405| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12249 Z= 0.141 Angle : 0.598 11.209 16584 Z= 0.307 Chirality : 0.040 0.130 1866 Planarity : 0.004 0.045 2135 Dihedral : 3.906 29.562 1649 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.77 % Favored : 91.96 % Rotamer: Outliers : 2.97 % Allowed : 24.09 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.23), residues: 1505 helix: 2.35 (0.20), residues: 767 sheet: -0.38 (0.62), residues: 76 loop : -1.67 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.013 0.001 TYR C 319 PHE 0.010 0.001 PHE A 144 TRP 0.008 0.001 TRP A 328 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00326 (12249) covalent geometry : angle 0.59845 (16584) hydrogen bonds : bond 0.04700 ( 556) hydrogen bonds : angle 3.60444 ( 1611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.80 seconds wall clock time: 32 minutes 57.82 seconds (1977.82 seconds total)