Starting phenix.real_space_refine on Tue Jun 10 21:22:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5m_39775/06_2025/8z5m_39775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5m_39775/06_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_39775/06_2025/8z5m_39775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5m_39775/06_2025/8z5m_39775.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5m_39775/06_2025/8z5m_39775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5m_39775/06_2025/8z5m_39775.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS: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: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 8.69, per 1000 atoms: 0.72 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.12 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: 3.74 Time building geometry restraints manager: 3.45 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: 7.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- 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 : 10.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP C 358 HIS 0.001 0.000 HIS A 959 PHE 0.028 0.001 PHE C 99 TYR 0.054 0.001 TYR C 94 ARG 0.004 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.15962 ( 556) hydrogen bonds : angle 4.67160 ( 1611) covalent geometry : bond 0.00394 (12249) covalent geometry : angle 0.64688 (16584) *********************** 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 : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8996 (mm) cc_final: 0.8769 (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: 0.6164 (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: 0.2306 time to fit residues: 68.7533 Evaluate side-chains 166 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 126 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.0020 chunk 60 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.163742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139873 restraints weight = 19320.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139247 restraints weight = 17786.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140050 restraints weight = 16562.987| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12249 Z= 0.129 Angle : 0.546 7.167 16584 Z= 0.283 Chirality : 0.040 0.155 1866 Planarity : 0.004 0.039 2135 Dihedral : 4.450 53.828 1660 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.64 % Favored : 93.29 % Rotamer: Outliers : 3.05 % Allowed : 22.33 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1505 helix: 3.00 (0.19), residues: 764 sheet: 0.91 (0.59), residues: 67 loop : -1.34 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 358 HIS 0.003 0.001 HIS A 237 PHE 0.009 0.001 PHE C 305 TYR 0.009 0.001 TYR C 320 ARG 0.003 0.000 ARG A1056 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 556) hydrogen bonds : angle 3.73017 ( 1611) covalent geometry : bond 0.00290 (12249) covalent geometry : angle 0.54573 (16584) *********************** 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 210 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7705 (tp) cc_final: 0.7445 (tt) REVERT: A 398 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6560 (pp) REVERT: A 1123 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: C 165 LYS cc_start: 0.8237 (ptpt) cc_final: 0.7683 (mttp) REVERT: C 220 MET cc_start: 0.8432 (ttt) cc_final: 0.8082 (ttt) REVERT: C 363 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 379 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6421 (tp) outliers start: 40 outliers final: 24 residues processed: 196 average time/residue: 0.2118 time to fit residues: 62.4691 Evaluate side-chains 179 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 448 THR 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 1123 TYR Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1182 SER 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 211 VAL 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 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 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.160066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133447 restraints weight = 19653.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134172 restraints weight = 16271.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135228 restraints weight = 13687.565| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12249 Z= 0.134 Angle : 0.546 7.953 16584 Z= 0.282 Chirality : 0.040 0.153 1866 Planarity : 0.004 0.052 2135 Dihedral : 3.790 35.228 1652 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 3.58 % Allowed : 22.18 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1505 helix: 2.69 (0.19), residues: 769 sheet: 0.62 (0.61), residues: 67 loop : -1.43 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 823 HIS 0.003 0.001 HIS A 959 PHE 0.009 0.001 PHE A 520 TYR 0.015 0.001 TYR C 319 ARG 0.005 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 556) hydrogen bonds : angle 3.57297 ( 1611) covalent geometry : bond 0.00305 (12249) covalent geometry : angle 0.54581 (16584) *********************** 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 213 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6185 (t80) REVERT: A 372 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8222 (pp) REVERT: A 398 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6886 (pp) REVERT: A 589 MET cc_start: 0.8398 (mtm) cc_final: 0.8050 (mtm) REVERT: A 617 SER cc_start: 0.9029 (m) cc_final: 0.8466 (t) REVERT: A 814 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: A 1123 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6400 (m-80) REVERT: C 165 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7624 (mttp) REVERT: C 220 MET cc_start: 0.8530 (ttt) cc_final: 0.8214 (ttt) REVERT: C 363 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7390 (tm-30) REVERT: C 379 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6712 (tp) REVERT: D 93 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7226 (t80) REVERT: D 116 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6208 (mmmm) outliers start: 47 outliers final: 26 residues processed: 200 average time/residue: 0.2140 time to fit residues: 63.6568 Evaluate side-chains 180 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 227 VAL 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 465 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 814 TYR 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 1215 LEU Chi-restraints excluded: chain C residue 37 CYS 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 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 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 132 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 134 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 HIS C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134558 restraints weight = 19268.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134020 restraints weight = 16876.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134209 restraints weight = 16778.096| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12249 Z= 0.130 Angle : 0.540 7.293 16584 Z= 0.278 Chirality : 0.039 0.129 1866 Planarity : 0.004 0.050 2135 Dihedral : 3.786 26.772 1650 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.71 % Favored : 93.16 % Rotamer: Outliers : 4.04 % Allowed : 23.17 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1505 helix: 2.53 (0.19), residues: 773 sheet: 0.56 (0.61), residues: 67 loop : -1.53 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 823 HIS 0.007 0.001 HIS C 39 PHE 0.009 0.001 PHE A 268 TYR 0.014 0.001 TYR C 319 ARG 0.005 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 556) hydrogen bonds : angle 3.54734 ( 1611) covalent geometry : bond 0.00299 (12249) covalent geometry : angle 0.54013 (16584) *********************** 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 204 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6230 (t80) REVERT: A 372 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8232 (pp) REVERT: A 398 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6775 (pp) REVERT: A 424 ASP cc_start: 0.8773 (p0) cc_final: 0.8313 (p0) REVERT: A 589 MET cc_start: 0.8563 (mtm) cc_final: 0.8236 (mtm) REVERT: A 617 SER cc_start: 0.8831 (m) cc_final: 0.8361 (t) REVERT: A 814 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: A 1123 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: C 220 MET cc_start: 0.8498 (ttt) cc_final: 0.8250 (ttt) REVERT: D 93 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7285 (t80) REVERT: D 125 MET cc_start: 0.6998 (mtp) cc_final: 0.6702 (mtp) outliers start: 53 outliers final: 34 residues processed: 188 average time/residue: 0.2155 time to fit residues: 60.9637 Evaluate side-chains 183 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 227 VAL 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 465 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 786 LEU 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 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 37 CYS Chi-restraints excluded: chain C residue 78 LEU 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 122 VAL Chi-restraints excluded: chain D residue 146 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 49 optimal weight: 0.3980 chunk 95 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.160409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134158 restraints weight = 19267.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133999 restraints weight = 16291.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135420 restraints weight = 14113.312| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12249 Z= 0.111 Angle : 0.523 7.560 16584 Z= 0.270 Chirality : 0.039 0.152 1866 Planarity : 0.004 0.048 2135 Dihedral : 3.711 27.202 1649 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.78 % Favored : 93.09 % Rotamer: Outliers : 3.96 % Allowed : 23.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1505 helix: 2.59 (0.19), residues: 769 sheet: 0.59 (0.61), residues: 67 loop : -1.53 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.002 0.000 HIS A 237 PHE 0.008 0.001 PHE A 268 TYR 0.011 0.001 TYR C 319 ARG 0.004 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 556) hydrogen bonds : angle 3.45618 ( 1611) covalent geometry : bond 0.00243 (12249) covalent geometry : angle 0.52337 (16584) *********************** 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 197 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6391 (t80) REVERT: A 372 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8229 (pp) REVERT: A 398 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6766 (pp) REVERT: A 424 ASP cc_start: 0.8879 (p0) cc_final: 0.8450 (p0) REVERT: A 589 MET cc_start: 0.8477 (mtm) cc_final: 0.8171 (mtm) REVERT: A 617 SER cc_start: 0.8923 (m) cc_final: 0.8459 (t) REVERT: A 814 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: A 1104 GLU cc_start: 0.7019 (pm20) cc_final: 0.6740 (pm20) REVERT: A 1123 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: C 220 MET cc_start: 0.8429 (ttt) cc_final: 0.8155 (ttt) REVERT: C 379 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6853 (tp) REVERT: D 93 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7357 (t80) REVERT: D 116 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6207 (mmmm) outliers start: 52 outliers final: 35 residues processed: 183 average time/residue: 0.2421 time to fit residues: 68.1432 Evaluate side-chains 182 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 227 VAL 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 465 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 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 1091 VAL 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 37 CYS Chi-restraints excluded: chain C residue 78 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 127 optimal weight: 0.0170 chunk 120 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.158287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133675 restraints weight = 19492.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133050 restraints weight = 18301.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133960 restraints weight = 16971.378| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12249 Z= 0.123 Angle : 0.535 7.593 16584 Z= 0.276 Chirality : 0.039 0.129 1866 Planarity : 0.004 0.047 2135 Dihedral : 3.772 27.868 1649 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.98 % Favored : 92.82 % Rotamer: Outliers : 4.19 % Allowed : 23.48 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1505 helix: 2.51 (0.19), residues: 774 sheet: 0.34 (0.61), residues: 67 loop : -1.60 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 823 HIS 0.002 0.001 HIS A 237 PHE 0.010 0.001 PHE A 268 TYR 0.011 0.001 TYR C 319 ARG 0.003 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 556) hydrogen bonds : angle 3.48675 ( 1611) covalent geometry : bond 0.00279 (12249) covalent geometry : angle 0.53501 (16584) *********************** 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 200 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6093 (t80) REVERT: A 372 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8302 (pp) REVERT: A 398 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6545 (pp) REVERT: A 424 ASP cc_start: 0.8694 (p0) cc_final: 0.8335 (p0) REVERT: A 589 MET cc_start: 0.8587 (mtm) cc_final: 0.8360 (mtm) REVERT: A 617 SER cc_start: 0.8828 (m) cc_final: 0.8379 (t) REVERT: A 814 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: A 1123 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6402 (m-80) REVERT: C 164 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8459 (pp) REVERT: C 379 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6833 (tp) REVERT: D 93 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7256 (t80) REVERT: D 116 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6149 (mmmm) outliers start: 55 outliers final: 39 residues processed: 183 average time/residue: 0.2120 time to fit residues: 58.1381 Evaluate side-chains 187 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 227 VAL 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 465 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 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 1091 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 21 GLU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 164 ILE 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 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 122 VAL 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 106 optimal weight: 0.0570 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 138 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.160592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134946 restraints weight = 19379.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135128 restraints weight = 15442.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136087 restraints weight = 14023.329| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2550 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= 0.102 Angle : 0.520 7.774 16584 Z= 0.267 Chirality : 0.038 0.129 1866 Planarity : 0.004 0.046 2135 Dihedral : 3.692 26.991 1649 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.96 % Rotamer: Outliers : 3.89 % Allowed : 23.78 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1505 helix: 2.59 (0.19), residues: 769 sheet: 0.41 (0.62), residues: 67 loop : -1.58 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.002 0.000 HIS A 237 PHE 0.009 0.001 PHE A 268 TYR 0.012 0.001 TYR C 319 ARG 0.008 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 556) hydrogen bonds : angle 3.37489 ( 1611) covalent geometry : bond 0.00219 (12249) covalent geometry : angle 0.52018 (16584) *********************** 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 196 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 372 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 398 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6573 (pp) REVERT: A 437 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6741 (t70) REVERT: A 530 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: A 589 MET cc_start: 0.8525 (mtm) cc_final: 0.8268 (mtm) REVERT: A 617 SER cc_start: 0.8926 (m) cc_final: 0.8447 (t) REVERT: A 814 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6118 (m-80) REVERT: A 904 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7250 (t80) REVERT: A 1123 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: C 92 ASP cc_start: 0.7020 (m-30) cc_final: 0.6705 (m-30) REVERT: C 164 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8477 (pp) REVERT: C 358 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8484 (m-10) REVERT: C 379 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6868 (tp) REVERT: D 93 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7308 (t80) outliers start: 51 outliers final: 28 residues processed: 182 average time/residue: 0.2190 time to fit residues: 60.8739 Evaluate side-chains 176 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 437 ASP Chi-restraints excluded: chain A residue 465 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 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 1091 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 1136 MET Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 164 ILE 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 328 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 358 TRP 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 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 19 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 109 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133636 restraints weight = 19470.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133608 restraints weight = 15903.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134649 restraints weight = 14053.033| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12249 Z= 0.103 Angle : 0.523 7.991 16584 Z= 0.267 Chirality : 0.038 0.147 1866 Planarity : 0.004 0.047 2135 Dihedral : 3.652 26.667 1649 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.78 % Favored : 92.96 % Rotamer: Outliers : 3.89 % Allowed : 23.93 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1505 helix: 2.54 (0.19), residues: 775 sheet: 0.50 (0.61), residues: 66 loop : -1.58 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.003 0.000 HIS A 90 PHE 0.009 0.001 PHE A 268 TYR 0.010 0.001 TYR C 319 ARG 0.006 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 556) hydrogen bonds : angle 3.35410 ( 1611) covalent geometry : bond 0.00224 (12249) covalent geometry : angle 0.52276 (16584) *********************** 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: 51 poor density : 138 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8311 (pp) REVERT: A 398 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6749 (pp) REVERT: A 437 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6804 (t70) REVERT: A 530 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: A 589 MET cc_start: 0.8452 (mtm) cc_final: 0.8221 (mtm) REVERT: A 617 SER cc_start: 0.9001 (m) cc_final: 0.8509 (t) REVERT: A 814 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: A 904 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 1123 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: A 1167 LYS cc_start: 0.7196 (tmtt) cc_final: 0.6964 (tmtt) REVERT: A 1169 LEU cc_start: 0.7702 (tp) cc_final: 0.7435 (tp) REVERT: C 164 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (pp) REVERT: C 358 TRP cc_start: 0.8884 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: C 379 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6919 (tp) REVERT: D 93 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7462 (t80) REVERT: D 116 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6359 (mmmm) outliers start: 51 outliers final: 34 residues processed: 174 average time/residue: 0.2130 time to fit residues: 56.8080 Evaluate side-chains 179 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 437 ASP Chi-restraints excluded: chain A residue 465 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 805 THR Chi-restraints excluded: chain A residue 814 TYR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1091 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 78 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 164 ILE 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 358 TRP 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 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 143 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135319 restraints weight = 19330.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133366 restraints weight = 18987.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134461 restraints weight = 18289.327| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12249 Z= 0.116 Angle : 0.542 8.383 16584 Z= 0.278 Chirality : 0.039 0.127 1866 Planarity : 0.004 0.046 2135 Dihedral : 3.729 27.343 1649 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.91 % Favored : 92.82 % Rotamer: Outliers : 3.73 % Allowed : 24.24 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1505 helix: 2.57 (0.19), residues: 768 sheet: 0.45 (0.63), residues: 66 loop : -1.59 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 90 PHE 0.009 0.001 PHE A 268 TYR 0.010 0.001 TYR C 319 ARG 0.004 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 556) hydrogen bonds : angle 3.39513 ( 1611) covalent geometry : bond 0.00259 (12249) covalent geometry : angle 0.54150 (16584) *********************** 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 189 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8342 (pp) REVERT: A 398 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6767 (pp) REVERT: A 530 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: A 589 MET cc_start: 0.8555 (mtm) cc_final: 0.8311 (mtm) REVERT: A 617 SER cc_start: 0.8898 (m) cc_final: 0.8434 (t) REVERT: A 814 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: A 904 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7219 (t80) REVERT: A 1123 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: A 1167 LYS cc_start: 0.7325 (tmtt) cc_final: 0.7086 (tmtt) REVERT: A 1169 LEU cc_start: 0.7686 (tp) cc_final: 0.7418 (tp) REVERT: C 164 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8503 (pp) REVERT: C 220 MET cc_start: 0.8363 (ttt) cc_final: 0.8132 (ttt) REVERT: C 358 TRP cc_start: 0.8810 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: C 379 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6970 (tp) REVERT: D 93 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7256 (t80) REVERT: D 116 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6120 (mmmm) outliers start: 49 outliers final: 33 residues processed: 173 average time/residue: 0.2039 time to fit residues: 54.2478 Evaluate side-chains 182 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 124 VAL 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 465 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 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 1091 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 21 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 164 ILE 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 358 TRP 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 93 PHE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 140 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.160314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133420 restraints weight = 19218.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133613 restraints weight = 15600.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133991 restraints weight = 13639.441| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2773 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= 0.104 Angle : 0.538 8.841 16584 Z= 0.276 Chirality : 0.038 0.150 1866 Planarity : 0.004 0.045 2135 Dihedral : 3.671 26.707 1649 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.78 % Favored : 92.96 % Rotamer: Outliers : 3.43 % Allowed : 24.70 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1505 helix: 2.51 (0.19), residues: 777 sheet: 0.57 (0.63), residues: 66 loop : -1.58 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.004 0.000 HIS A 90 PHE 0.009 0.001 PHE A 268 TYR 0.010 0.001 TYR C 319 ARG 0.004 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 556) hydrogen bonds : angle 3.33570 ( 1611) covalent geometry : bond 0.00222 (12249) covalent geometry : angle 0.53785 (16584) ********************** 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 183 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 398 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6779 (pp) REVERT: A 530 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: A 589 MET cc_start: 0.8457 (mtm) cc_final: 0.8254 (mtm) REVERT: A 617 SER cc_start: 0.8969 (m) cc_final: 0.8473 (t) REVERT: A 814 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: A 904 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 1123 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: A 1167 LYS cc_start: 0.7407 (tmtt) cc_final: 0.7145 (tmtt) REVERT: A 1169 LEU cc_start: 0.7638 (tp) cc_final: 0.7391 (tp) REVERT: C 92 ASP cc_start: 0.7161 (m-30) cc_final: 0.6948 (m-30) REVERT: C 164 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 220 MET cc_start: 0.8367 (ttt) cc_final: 0.8131 (ttt) REVERT: C 358 TRP cc_start: 0.8879 (OUTLIER) cc_final: 0.8441 (m-10) REVERT: C 379 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7000 (tp) REVERT: D 93 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7227 (t80) REVERT: D 101 ILE cc_start: 0.5949 (mp) cc_final: 0.5475 (mp) REVERT: D 116 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6298 (mmmm) outliers start: 45 outliers final: 32 residues processed: 170 average time/residue: 0.2130 time to fit residues: 55.3196 Evaluate side-chains 179 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 172 ILE 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 372 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 465 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 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 1091 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 78 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 164 ILE 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 328 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 358 TRP 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 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.159626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135209 restraints weight = 19366.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134660 restraints weight = 18702.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135800 restraints weight = 17526.656| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12249 Z= 0.110 Angle : 0.546 8.733 16584 Z= 0.280 Chirality : 0.038 0.155 1866 Planarity : 0.004 0.045 2135 Dihedral : 3.669 26.537 1649 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.96 % Rotamer: Outliers : 3.58 % Allowed : 24.70 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1505 helix: 2.55 (0.19), residues: 771 sheet: 0.54 (0.63), residues: 66 loop : -1.60 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.004 0.000 HIS A 90 PHE 0.008 0.001 PHE A 268 TYR 0.008 0.001 TYR A 313 ARG 0.004 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 556) hydrogen bonds : angle 3.33780 ( 1611) covalent geometry : bond 0.00241 (12249) covalent geometry : angle 0.54594 (16584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3744.21 seconds wall clock time: 65 minutes 35.72 seconds (3935.72 seconds total)