Starting phenix.real_space_refine on Fri Feb 6 16:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mgg_48255/02_2026/9mgg_48255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mgg_48255/02_2026/9mgg_48255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mgg_48255/02_2026/9mgg_48255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mgg_48255/02_2026/9mgg_48255.map" model { file = "/net/cci-nas-00/data/ceres_data/9mgg_48255/02_2026/9mgg_48255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mgg_48255/02_2026/9mgg_48255.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 8320 2.51 5 N 2295 2.21 5 O 2638 1.98 5 H 12414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25706 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 10087 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 13, 'HIS:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 10, 'ASN:plan1': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 257 Chain: "C" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 717 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 7, 'TRANS': 43} Chain: "D" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3426 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1355 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "B" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5223 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4898 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 17, 'TRANS': 303} Chain breaks: 1 Time building chain proxies: 4.95, per 1000 atoms: 0.19 Number of scatterers: 25706 At special positions: 0 Unit cell: (134.46, 126.16, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 2638 8.00 N 2295 7.00 C 8320 6.00 H 12414 1.00 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: 2.21 Conformation dependent library (CDL) restraints added in 916.0 milliseconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 18 sheets defined 22.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.724A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.726A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 361 through 369 removed outlier: 4.094A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 34 through 45 removed outlier: 4.221A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.585A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.525A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 5.978A pdb=" N GLN D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY D 126 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.607A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.589A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 removed outlier: 4.365A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'F' and resid 497 through 499 No H-bonds generated for 'chain 'F' and resid 497 through 499' Processing helix chain 'F' and resid 542 through 553 Processing helix chain 'F' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 124 removed outlier: 4.072A pdb=" N GLU A 123 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.837A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 244 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 245 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 274 removed outlier: 6.449A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.183A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.799A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.636A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 12.399A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.961A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP A 627 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 428 " --> pdb=" O ILE F 806 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA F 770 " --> pdb=" O GLN F 789 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 791 " --> pdb=" O MET F 768 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N MET F 768 " --> pdb=" O PHE F 791 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR F 735 " --> pdb=" O THR F 720 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET F 711 " --> pdb=" O GLY F 636 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL F 628 " --> pdb=" O ILE F 719 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY F 575 " --> pdb=" O ARG F 526 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG F 526 " --> pdb=" O GLY F 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY F 510 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL F 483 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR F 477 " --> pdb=" O VAL F 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.961A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP A 627 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 428 " --> pdb=" O ILE F 806 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA F 770 " --> pdb=" O GLN F 789 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 791 " --> pdb=" O MET F 768 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N MET F 768 " --> pdb=" O PHE F 791 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR F 735 " --> pdb=" O THR F 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 673 removed outlier: 5.306A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.648A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 96 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU E 101 " --> pdb=" O ASN E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.213A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.672A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.520A pdb=" N GLN B 172 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.890A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.583A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 287 through 292 removed outlier: 6.845A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL B 299 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 337 through 340 removed outlier: 6.766A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 671 through 673 removed outlier: 3.706A pdb=" N ALA F 672 " --> pdb=" O SER F 702 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2217 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: 6.45 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12411 1.02 - 1.22: 9 1.22 - 1.42: 5999 1.42 - 1.62: 7515 1.62 - 1.82: 75 Bond restraints: 26009 Sorted by residual: bond pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.21e-02 6.83e+03 1.11e+01 bond pdb=" N PHE B 367 " pdb=" CA PHE B 367 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.23e-02 6.61e+03 9.17e+00 bond pdb=" C PRO D 31 " pdb=" O PRO D 31 " ideal model delta sigma weight residual 1.240 1.207 0.033 1.12e-02 7.97e+03 8.91e+00 bond pdb=" N ILE A 668 " pdb=" CA ILE A 668 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.60e+00 bond pdb=" N THR B 369 " pdb=" CA THR B 369 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.33e+00 ... (remaining 26004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 45526 2.03 - 4.07: 813 4.07 - 6.10: 73 6.10 - 8.14: 12 8.14 - 10.17: 4 Bond angle restraints: 46428 Sorted by residual: angle pdb=" N LEU A 223 " pdb=" CA LEU A 223 " pdb=" C LEU A 223 " ideal model delta sigma weight residual 111.36 106.38 4.98 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N GLN B 368 " pdb=" CA GLN B 368 " pdb=" C GLN B 368 " ideal model delta sigma weight residual 113.02 106.40 6.62 1.49e+00 4.50e-01 1.97e+01 angle pdb=" CA VAL A 364 " pdb=" C VAL A 364 " pdb=" O VAL A 364 " ideal model delta sigma weight residual 120.85 116.22 4.63 1.06e+00 8.90e-01 1.90e+01 angle pdb=" N GLN A 466 " pdb=" CA GLN A 466 " pdb=" C GLN A 466 " ideal model delta sigma weight residual 108.26 115.44 -7.18 1.66e+00 3.63e-01 1.87e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 120.75 116.48 4.27 1.03e+00 9.43e-01 1.72e+01 ... (remaining 46423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10927 17.69 - 35.37: 978 35.37 - 53.06: 285 53.06 - 70.75: 79 70.75 - 88.44: 17 Dihedral angle restraints: 12286 sinusoidal: 6526 harmonic: 5760 Sorted by residual: dihedral pdb=" CA PRO F 647 " pdb=" C PRO F 647 " pdb=" N PHE F 648 " pdb=" CA PHE F 648 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA TYR A 454 " pdb=" C TYR A 454 " pdb=" N ALA A 455 " pdb=" CA ALA A 455 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN A 475 " pdb=" C ASN A 475 " pdb=" N PRO A 476 " pdb=" CA PRO A 476 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 12283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1335 0.045 - 0.090: 405 0.090 - 0.134: 134 0.134 - 0.179: 18 0.179 - 0.224: 3 Chirality restraints: 1895 Sorted by residual: chirality pdb=" CA LEU A 247 " pdb=" N LEU A 247 " pdb=" C LEU A 247 " pdb=" CB LEU A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA HIS B 324 " pdb=" N HIS B 324 " pdb=" C HIS B 324 " pdb=" CB HIS B 324 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 1892 not shown) Planarity restraints: 4159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 30 " -0.254 2.00e-02 2.50e+03 3.27e-01 1.60e+03 pdb=" CG ASN D 30 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 30 " 0.242 2.00e-02 2.50e+03 pdb=" ND2 ASN D 30 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN D 30 " 0.503 2.00e-02 2.50e+03 pdb="HD22 ASN D 30 " -0.515 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 368 " -0.092 2.00e-02 2.50e+03 9.43e-02 1.33e+02 pdb=" CD GLN B 368 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 368 " 0.081 2.00e-02 2.50e+03 pdb=" NE2 GLN B 368 " 0.007 2.00e-02 2.50e+03 pdb="HE21 GLN B 368 " 0.133 2.00e-02 2.50e+03 pdb="HE22 GLN B 368 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 542 " 0.063 2.00e-02 2.50e+03 8.15e-02 9.96e+01 pdb=" CD GLN A 542 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN A 542 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 542 " -0.131 2.00e-02 2.50e+03 pdb="HE21 GLN A 542 " -0.012 2.00e-02 2.50e+03 pdb="HE22 GLN A 542 " 0.128 2.00e-02 2.50e+03 ... (remaining 4156 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 1682 2.20 - 2.80: 51354 2.80 - 3.40: 68131 3.40 - 4.00: 87102 4.00 - 4.60: 133228 Nonbonded interactions: 341497 Sorted by model distance: nonbonded pdb=" O ASP B 271 " pdb=" H GLY B 275 " model vdw 1.595 2.450 nonbonded pdb=" OE1 GLN D 50 " pdb=" H GLN D 50 " model vdw 1.601 2.450 nonbonded pdb=" HG SER F 778 " pdb=" O GLY F 781 " model vdw 1.601 2.450 nonbonded pdb=" O ALA B 235 " pdb=" HG1 THR B 236 " model vdw 1.604 2.450 nonbonded pdb=" OD1 ASP B 138 " pdb=" HG1 THR B 140 " model vdw 1.612 2.450 ... (remaining 341492 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.060 13595 Z= 0.222 Angle : 0.839 9.164 18420 Z= 0.495 Chirality : 0.049 0.224 1895 Planarity : 0.008 0.108 2475 Dihedral : 15.139 88.436 4800 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 1.03 % Allowed : 17.66 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 1750 helix: -1.03 (0.23), residues: 353 sheet: -0.05 (0.21), residues: 538 loop : -1.82 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG A 767 TYR 0.029 0.004 TYR F 522 PHE 0.024 0.003 PHE A 802 TRP 0.031 0.004 TRP A 576 HIS 0.013 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00402 (13595) covalent geometry : angle 0.83946 (18420) hydrogen bonds : bond 0.21349 ( 625) hydrogen bonds : angle 9.00568 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 775 GLN cc_start: 0.7942 (mp10) cc_final: 0.7578 (mp10) REVERT: F 646 MET cc_start: 0.7674 (ttp) cc_final: 0.7291 (ptm) outliers start: 14 outliers final: 5 residues processed: 273 average time/residue: 0.2815 time to fit residues: 106.7724 Evaluate side-chains 246 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 240 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 610 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.143822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112924 restraints weight = 83858.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115541 restraints weight = 36799.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118056 restraints weight = 24302.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.118424 restraints weight = 20535.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.118407 restraints weight = 17784.136| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13595 Z= 0.144 Angle : 0.662 6.084 18420 Z= 0.363 Chirality : 0.045 0.162 1895 Planarity : 0.005 0.075 2475 Dihedral : 6.968 59.501 1942 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.07 % Allowed : 16.26 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1750 helix: 0.45 (0.26), residues: 358 sheet: -0.24 (0.20), residues: 565 loop : -1.50 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 233 TYR 0.018 0.001 TYR F 794 PHE 0.021 0.002 PHE F 570 TRP 0.021 0.001 TRP A 576 HIS 0.008 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00298 (13595) covalent geometry : angle 0.66210 (18420) hydrogen bonds : bond 0.05557 ( 625) hydrogen bonds : angle 6.25224 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7374 (mtt90) cc_final: 0.7153 (mtt90) REVERT: A 775 GLN cc_start: 0.7772 (mp10) cc_final: 0.7207 (mp10) REVERT: E 50 MET cc_start: 0.7193 (ttm) cc_final: 0.6917 (ttm) REVERT: F 646 MET cc_start: 0.7572 (ttp) cc_final: 0.7321 (ptm) outliers start: 28 outliers final: 20 residues processed: 257 average time/residue: 0.2797 time to fit residues: 101.3826 Evaluate side-chains 246 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 713 VAL Chi-restraints excluded: chain F residue 795 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 72 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 50.0000 chunk 6 optimal weight: 30.0000 chunk 160 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 50.0000 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN B 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.142818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111651 restraints weight = 83183.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114181 restraints weight = 37907.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116210 restraints weight = 24993.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.116837 restraints weight = 20941.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.116866 restraints weight = 18587.562| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13595 Z= 0.177 Angle : 0.614 6.286 18420 Z= 0.337 Chirality : 0.043 0.206 1895 Planarity : 0.004 0.058 2475 Dihedral : 6.338 53.302 1938 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.88 % Allowed : 15.89 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.19), residues: 1750 helix: 0.91 (0.27), residues: 361 sheet: -0.45 (0.20), residues: 565 loop : -1.44 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 49 TYR 0.019 0.002 TYR D 77 PHE 0.021 0.002 PHE F 570 TRP 0.019 0.001 TRP A 576 HIS 0.007 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00371 (13595) covalent geometry : angle 0.61393 (18420) hydrogen bonds : bond 0.04651 ( 625) hydrogen bonds : angle 5.51279 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7247 (tpp) REVERT: D 183 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 218 MET cc_start: 0.8473 (tpp) cc_final: 0.8268 (ttm) REVERT: B 85 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6565 (p0) REVERT: F 652 PHE cc_start: 0.7792 (m-80) cc_final: 0.7552 (m-80) outliers start: 39 outliers final: 30 residues processed: 257 average time/residue: 0.2807 time to fit residues: 101.5200 Evaluate side-chains 256 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 536 LEU Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 585 TYR Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 713 VAL Chi-restraints excluded: chain F residue 783 LEU Chi-restraints excluded: chain F residue 795 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN E 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.135332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102930 restraints weight = 84952.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104765 restraints weight = 45836.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.106169 restraints weight = 31643.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107002 restraints weight = 27331.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107041 restraints weight = 23420.717| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13595 Z= 0.342 Angle : 0.708 6.335 18420 Z= 0.395 Chirality : 0.046 0.170 1895 Planarity : 0.005 0.054 2475 Dihedral : 6.523 55.875 1938 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.92 % Allowed : 16.85 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1750 helix: 0.68 (0.27), residues: 359 sheet: -0.81 (0.21), residues: 548 loop : -1.74 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 488 TYR 0.028 0.002 TYR A 578 PHE 0.023 0.002 PHE F 570 TRP 0.020 0.002 TRP A 576 HIS 0.008 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00726 (13595) covalent geometry : angle 0.70815 (18420) hydrogen bonds : bond 0.04996 ( 625) hydrogen bonds : angle 5.72392 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.8077 (mtm) cc_final: 0.7472 (tpp) REVERT: D 183 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 248 ASP cc_start: 0.8202 (m-30) cc_final: 0.7991 (m-30) REVERT: F 610 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8279 (ttmm) REVERT: F 652 PHE cc_start: 0.7995 (m-80) cc_final: 0.7443 (m-80) outliers start: 53 outliers final: 45 residues processed: 248 average time/residue: 0.2761 time to fit residues: 96.5446 Evaluate side-chains 259 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 536 LEU Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 585 TYR Chi-restraints excluded: chain F residue 599 VAL Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 713 VAL Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 783 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 165 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 12 optimal weight: 40.0000 chunk 172 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 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 = 0.4053 r_free = 0.4053 target = 0.138931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104636 restraints weight = 83230.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108815 restraints weight = 41031.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111529 restraints weight = 26254.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113238 restraints weight = 19736.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114404 restraints weight = 16486.226| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13595 Z= 0.130 Angle : 0.597 5.788 18420 Z= 0.323 Chirality : 0.044 0.162 1895 Planarity : 0.004 0.054 2475 Dihedral : 6.054 56.391 1938 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.10 % Allowed : 18.11 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1750 helix: 1.30 (0.27), residues: 359 sheet: -0.69 (0.21), residues: 546 loop : -1.49 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 49 TYR 0.016 0.001 TYR B 345 PHE 0.015 0.001 PHE F 570 TRP 0.020 0.001 TRP A 576 HIS 0.010 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00280 (13595) covalent geometry : angle 0.59687 (18420) hydrogen bonds : bond 0.04149 ( 625) hydrogen bonds : angle 5.10444 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7163 (tpp) REVERT: A 661 ARG cc_start: 0.7523 (mtt90) cc_final: 0.7241 (mtt90) REVERT: D 183 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8102 (tm-30) REVERT: F 652 PHE cc_start: 0.7979 (m-80) cc_final: 0.7715 (m-80) outliers start: 42 outliers final: 38 residues processed: 258 average time/residue: 0.2755 time to fit residues: 101.0395 Evaluate side-chains 263 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 536 LEU Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 585 TYR Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 783 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 50.0000 chunk 1 optimal weight: 40.0000 chunk 124 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN B 368 GLN ** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.138850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.108055 restraints weight = 84157.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109957 restraints weight = 40509.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.111282 restraints weight = 29526.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111961 restraints weight = 28642.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111963 restraints weight = 23690.671| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13595 Z= 0.129 Angle : 0.575 7.360 18420 Z= 0.310 Chirality : 0.043 0.158 1895 Planarity : 0.004 0.053 2475 Dihedral : 5.815 56.717 1938 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.25 % Allowed : 18.48 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1750 helix: 1.51 (0.27), residues: 359 sheet: -0.69 (0.21), residues: 546 loop : -1.45 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 49 TYR 0.018 0.001 TYR B 345 PHE 0.015 0.001 PHE F 570 TRP 0.019 0.001 TRP A 576 HIS 0.009 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00281 (13595) covalent geometry : angle 0.57542 (18420) hydrogen bonds : bond 0.03875 ( 625) hydrogen bonds : angle 4.92044 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 552 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7326 (tpp) REVERT: D 183 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7762 (tm-30) REVERT: F 610 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7971 (mtpp) REVERT: F 652 PHE cc_start: 0.7968 (m-80) cc_final: 0.7534 (m-80) REVERT: F 800 GLU cc_start: 0.7957 (tt0) cc_final: 0.7633 (tt0) outliers start: 44 outliers final: 35 residues processed: 256 average time/residue: 0.2659 time to fit residues: 96.6425 Evaluate side-chains 263 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 536 LEU Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 783 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 23 optimal weight: 7.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.137398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106715 restraints weight = 83805.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108403 restraints weight = 39868.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109022 restraints weight = 30237.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109778 restraints weight = 28922.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109833 restraints weight = 25307.058| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13595 Z= 0.188 Angle : 0.591 7.128 18420 Z= 0.322 Chirality : 0.043 0.146 1895 Planarity : 0.004 0.051 2475 Dihedral : 5.822 57.813 1938 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.33 % Allowed : 18.77 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1750 helix: 1.47 (0.27), residues: 359 sheet: -0.75 (0.21), residues: 548 loop : -1.50 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 233 TYR 0.019 0.002 TYR A 578 PHE 0.015 0.001 PHE F 570 TRP 0.018 0.001 TRP A 576 HIS 0.008 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00401 (13595) covalent geometry : angle 0.59079 (18420) hydrogen bonds : bond 0.03996 ( 625) hydrogen bonds : angle 4.97418 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7371 (tpp) REVERT: D 183 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7868 (tm-30) REVERT: F 652 PHE cc_start: 0.7998 (m-80) cc_final: 0.7760 (m-80) outliers start: 45 outliers final: 38 residues processed: 251 average time/residue: 0.2997 time to fit residues: 106.2092 Evaluate side-chains 256 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 783 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 142 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101451 restraints weight = 84401.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105811 restraints weight = 38821.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108733 restraints weight = 23994.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110544 restraints weight = 17762.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111652 restraints weight = 14703.620| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13595 Z= 0.244 Angle : 0.637 10.287 18420 Z= 0.348 Chirality : 0.044 0.157 1895 Planarity : 0.004 0.066 2475 Dihedral : 5.961 59.327 1938 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.55 % Allowed : 19.07 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1750 helix: 1.35 (0.27), residues: 359 sheet: -0.87 (0.21), residues: 553 loop : -1.67 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 77 TYR 0.023 0.002 TYR A 578 PHE 0.025 0.002 PHE B 289 TRP 0.017 0.001 TRP A 576 HIS 0.008 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00521 (13595) covalent geometry : angle 0.63690 (18420) hydrogen bonds : bond 0.04219 ( 625) hydrogen bonds : angle 5.11379 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7330 (tpp) REVERT: D 183 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8297 (tm-30) REVERT: F 583 ARG cc_start: 0.7688 (mpt180) cc_final: 0.7437 (mpt180) REVERT: F 652 PHE cc_start: 0.8067 (m-80) cc_final: 0.7752 (m-80) outliers start: 48 outliers final: 46 residues processed: 242 average time/residue: 0.2962 time to fit residues: 101.3521 Evaluate side-chains 258 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 713 VAL Chi-restraints excluded: chain F residue 741 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 126 optimal weight: 0.1980 chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.138401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106358 restraints weight = 84636.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108686 restraints weight = 41602.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109946 restraints weight = 28125.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110732 restraints weight = 24646.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110891 restraints weight = 20932.339| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13595 Z= 0.117 Angle : 0.580 7.919 18420 Z= 0.309 Chirality : 0.043 0.151 1895 Planarity : 0.004 0.051 2475 Dihedral : 5.625 59.979 1936 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.88 % Allowed : 19.59 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1750 helix: 1.73 (0.27), residues: 359 sheet: -0.72 (0.21), residues: 547 loop : -1.45 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 49 TYR 0.016 0.001 TYR D 77 PHE 0.023 0.001 PHE B 289 TRP 0.020 0.001 TRP A 576 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00257 (13595) covalent geometry : angle 0.57980 (18420) hydrogen bonds : bond 0.03729 ( 625) hydrogen bonds : angle 4.74564 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: A 661 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7152 (mtt90) REVERT: A 739 TRP cc_start: 0.7890 (t60) cc_final: 0.7680 (t60) REVERT: D 183 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8184 (tm-30) REVERT: F 652 PHE cc_start: 0.8035 (m-80) cc_final: 0.7761 (m-80) outliers start: 39 outliers final: 36 residues processed: 244 average time/residue: 0.2960 time to fit residues: 101.4984 Evaluate side-chains 251 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 741 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** F 606 ASN ** 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 = 0.4034 r_free = 0.4034 target = 0.137547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105075 restraints weight = 86226.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108227 restraints weight = 40595.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110563 restraints weight = 26323.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111358 restraints weight = 22108.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111167 restraints weight = 18250.167| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13595 Z= 0.113 Angle : 0.573 7.502 18420 Z= 0.305 Chirality : 0.043 0.153 1895 Planarity : 0.004 0.070 2475 Dihedral : 5.459 59.158 1936 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.59 % Allowed : 20.10 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1750 helix: 1.89 (0.27), residues: 359 sheet: -0.63 (0.21), residues: 549 loop : -1.37 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 49 TYR 0.017 0.001 TYR B 345 PHE 0.014 0.001 PHE F 570 TRP 0.022 0.001 TRP A 576 HIS 0.007 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00252 (13595) covalent geometry : angle 0.57325 (18420) hydrogen bonds : bond 0.03534 ( 625) hydrogen bonds : angle 4.59682 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7326 (tpp) REVERT: A 661 ARG cc_start: 0.7392 (mtt90) cc_final: 0.7060 (mtt90) REVERT: A 739 TRP cc_start: 0.7830 (t60) cc_final: 0.7621 (t60) REVERT: D 183 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8229 (tm-30) REVERT: F 645 GLU cc_start: 0.7713 (tt0) cc_final: 0.6135 (mm-30) REVERT: F 652 PHE cc_start: 0.7981 (m-80) cc_final: 0.7712 (m-80) outliers start: 35 outliers final: 31 residues processed: 239 average time/residue: 0.2835 time to fit residues: 95.4986 Evaluate side-chains 246 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 491 TYR Chi-restraints excluded: chain F residue 517 PHE Chi-restraints excluded: chain F residue 522 TYR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 610 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 109 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 13 optimal weight: 50.0000 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.137360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.106502 restraints weight = 84542.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108322 restraints weight = 40413.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.108933 restraints weight = 29440.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109835 restraints weight = 27611.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.110296 restraints weight = 24156.403| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13595 Z= 0.181 Angle : 0.601 7.573 18420 Z= 0.323 Chirality : 0.042 0.153 1895 Planarity : 0.004 0.058 2475 Dihedral : 5.516 58.082 1936 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.51 % Allowed : 20.03 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1750 helix: 1.83 (0.27), residues: 359 sheet: -0.68 (0.21), residues: 548 loop : -1.48 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 583 TYR 0.018 0.002 TYR A 578 PHE 0.015 0.001 PHE F 570 TRP 0.020 0.001 TRP A 576 HIS 0.008 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00392 (13595) covalent geometry : angle 0.60098 (18420) hydrogen bonds : bond 0.03821 ( 625) hydrogen bonds : angle 4.75034 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.54 seconds wall clock time: 73 minutes 19.26 seconds (4399.26 seconds total)