Starting phenix.real_space_refine on Thu Feb 5 10:13:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpc_74526/02_2026/9zpc_74526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpc_74526/02_2026/9zpc_74526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zpc_74526/02_2026/9zpc_74526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpc_74526/02_2026/9zpc_74526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zpc_74526/02_2026/9zpc_74526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpc_74526/02_2026/9zpc_74526.map" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 10378 2.51 5 N 2831 2.21 5 O 2980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.01s 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: 16275 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8350 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 51, 'TRANS': 993} Chain breaks: 8 Chain: "B" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2034 Classifications: {'peptide': 250} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 236} Chain breaks: 2 Chain: "C" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3153 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 11, 'TRANS': 373} Chain breaks: 4 Chain: "D" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2708 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 320} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13583 SG CYS D 18 55.543 46.819 34.447 1.00109.73 S ATOM 14089 SG CYS D 140 55.429 44.754 38.891 1.00111.96 S Time building chain proxies: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16275 At special positions: 0 Unit cell: (74.408, 147.768, 233.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 82 16.00 P 2 15.00 Mg 1 11.99 O 2980 8.00 N 2831 7.00 C 10378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 727.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 140 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 18 " 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 18 sheets defined 51.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 67 through 79 removed outlier: 4.327A pdb=" N LEU A 71 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 121 through 142 Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.517A pdb=" N ASP A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.652A pdb=" N ASP A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 317 through 323 removed outlier: 3.839A pdb=" N TYR A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.976A pdb=" N PHE A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 removed outlier: 3.503A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 removed outlier: 3.592A pdb=" N VAL A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 473 removed outlier: 4.348A pdb=" N HIS A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 501 removed outlier: 4.525A pdb=" N ALA A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 547 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 560 through 569 removed outlier: 4.337A pdb=" N VAL A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A 567 " --> pdb=" O ARG A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 4.338A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 584 " --> pdb=" O HIS A 580 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 608 removed outlier: 3.725A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 625 Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 628 through 645 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 669 through 686 Processing helix chain 'A' and resid 687 through 700 Proline residue: A 697 - end of helix Processing helix chain 'A' and resid 712 through 720 Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.925A pdb=" N SER A 735 " --> pdb=" O TYR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 754 removed outlier: 3.959A pdb=" N LEU A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 removed outlier: 3.608A pdb=" N ALA A 768 " --> pdb=" O ASP A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 790 through 803 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'B' and resid 34 through 41 removed outlier: 3.868A pdb=" N VAL B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.842A pdb=" N MET B 135 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 4.427A pdb=" N LYS B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 212 removed outlier: 3.616A pdb=" N SER B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.581A pdb=" N SER B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 192 through 329 removed outlier: 4.663A pdb=" N SER C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 379 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 418 through 441 Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'D' and resid 28 through 34 Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'D' and resid 137 through 171 Processing helix chain 'D' and resid 176 through 267 removed outlier: 3.504A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 299 through 322 removed outlier: 3.503A pdb=" N ILE D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 387 removed outlier: 3.516A pdb=" N ASP D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 447 removed outlier: 3.857A pdb=" N PHE D 447 " --> pdb=" O VAL D 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 985 through 989 removed outlier: 3.915A pdb=" N ALA A 987 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A1356 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1348 " --> pdb=" O ASP A1334 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A1334 " --> pdb=" O ALA A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 996 through 1002 removed outlier: 3.630A pdb=" N ARG A 998 " --> pdb=" O CYS A1011 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1048 through 1050 Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 6.086A pdb=" N LEU A1121 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR A1134 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A1123 " --> pdb=" O ALA A1132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1144 through 1149 removed outlier: 3.531A pdb=" N SER A1146 " --> pdb=" O GLY A1159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 3.868A pdb=" N GLU A1209 " --> pdb=" O VAL A1204 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP A1214 " --> pdb=" O ARG A1220 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG A1220 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A1299 " --> pdb=" O ARG A1221 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1242 through 1250 Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AB2, first strand: chain 'B' and resid 89 through 96 removed outlier: 3.933A pdb=" N VAL B 19 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE B 23 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU B 220 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET B 215 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 68 through 69 removed outlier: 4.328A pdb=" N GLY B 123 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 112 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR B 114 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B 119 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 51 Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.793A pdb=" N LYS C 132 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 332 through 333 removed outlier: 4.545A pdb=" N TYR C 339 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AB8, first strand: chain 'D' and resid 277 through 279 Processing sheet with id=AB9, first strand: chain 'D' and resid 396 through 397 897 hydrogen bonds defined for protein. 2559 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: 2.24 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5289 1.34 - 1.46: 3407 1.46 - 1.58: 7787 1.58 - 1.70: 3 1.70 - 1.82: 124 Bond restraints: 16610 Sorted by residual: bond pdb=" C TRP A 161 " pdb=" N VAL A 162 " ideal model delta sigma weight residual 1.329 1.277 0.053 1.15e-02 7.56e+03 2.09e+01 bond pdb=" N ILE C 53 " pdb=" CA ILE C 53 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.49e+00 bond pdb=" N GLN A1092 " pdb=" CA GLN A1092 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.08e+00 bond pdb=" N VAL A1117 " pdb=" CA VAL A1117 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" N HIS A 990 " pdb=" CA HIS A 990 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.82e+00 ... (remaining 16605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 21846 2.53 - 5.06: 536 5.06 - 7.59: 50 7.59 - 10.13: 13 10.13 - 12.66: 6 Bond angle restraints: 22451 Sorted by residual: angle pdb=" C ASP A1095 " pdb=" CA ASP A1095 " pdb=" CB ASP A1095 " ideal model delta sigma weight residual 110.11 119.43 -9.32 1.89e+00 2.80e-01 2.43e+01 angle pdb=" N VAL A1117 " pdb=" CA VAL A1117 " pdb=" C VAL A1117 " ideal model delta sigma weight residual 110.62 105.77 4.85 1.02e+00 9.61e-01 2.26e+01 angle pdb=" N HIS A 990 " pdb=" CA HIS A 990 " pdb=" C HIS A 990 " ideal model delta sigma weight residual 112.57 107.67 4.90 1.13e+00 7.83e-01 1.88e+01 angle pdb=" N ALA A 732 " pdb=" CA ALA A 732 " pdb=" C ALA A 732 " ideal model delta sigma weight residual 111.40 106.23 5.17 1.22e+00 6.72e-01 1.79e+01 angle pdb=" C PHE D 325 " pdb=" N GLN D 326 " pdb=" CA GLN D 326 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 ... (remaining 22446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.43: 9439 22.43 - 44.86: 556 44.86 - 67.29: 48 67.29 - 89.73: 25 89.73 - 112.16: 1 Dihedral angle restraints: 10069 sinusoidal: 4183 harmonic: 5886 Sorted by residual: dihedral pdb=" O5' GDP A1501 " pdb=" O3A GDP A1501 " pdb=" PA GDP A1501 " pdb=" PB GDP A1501 " ideal model delta sinusoidal sigma weight residual 180.02 67.86 112.16 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N TYR A 459 " pdb=" CA TYR A 459 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" C ASP A1095 " pdb=" N ASP A1095 " pdb=" CA ASP A1095 " pdb=" CB ASP A1095 " ideal model delta harmonic sigma weight residual -122.60 -136.64 14.04 0 2.50e+00 1.60e-01 3.15e+01 ... (remaining 10066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2218 0.087 - 0.174: 260 0.174 - 0.260: 17 0.260 - 0.347: 4 0.347 - 0.434: 2 Chirality restraints: 2501 Sorted by residual: chirality pdb=" CA ASP A1095 " pdb=" N ASP A1095 " pdb=" C ASP A1095 " pdb=" CB ASP A1095 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ILE A 738 " pdb=" N ILE A 738 " pdb=" C ILE A 738 " pdb=" CB ILE A 738 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ILE A1059 " pdb=" N ILE A1059 " pdb=" C ILE A1059 " pdb=" CB ILE A1059 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2498 not shown) Planarity restraints: 2857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1199 " 0.034 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP A1199 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A1199 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A1199 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A1199 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1199 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1199 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1199 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1199 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A1199 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 459 " 0.002 2.00e-02 2.50e+03 1.88e-02 7.09e+00 pdb=" CG TYR A 459 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 459 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 459 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 459 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 459 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 459 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 459 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 692 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C TYR A 692 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR A 692 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS A 693 " 0.015 2.00e-02 2.50e+03 ... (remaining 2854 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 422 2.68 - 3.24: 17222 3.24 - 3.79: 27085 3.79 - 4.35: 35437 4.35 - 4.90: 57197 Nonbonded interactions: 137363 Sorted by model distance: nonbonded pdb=" O LYS A1046 " pdb=" OG1 THR A1047 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP B 112 " pdb=" N VAL B 113 " model vdw 2.184 3.120 nonbonded pdb=" NH1 ARG A 113 " pdb=" O PRO A 118 " model vdw 2.201 3.120 nonbonded pdb=" O LYS D 430 " pdb=" OG1 THR D 434 " model vdw 2.208 3.040 nonbonded pdb=" O VAL A 381 " pdb=" OG SER A 384 " model vdw 2.209 3.040 ... (remaining 137358 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 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 : 0.008 0.446 16612 Z= 0.387 Angle : 0.942 12.658 22451 Z= 0.528 Chirality : 0.057 0.434 2501 Planarity : 0.005 0.059 2857 Dihedral : 14.258 112.158 6239 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.06 % Allowed : 0.95 % Favored : 99.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.44 % 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: -0.96 (0.18), residues: 1964 helix: 0.31 (0.16), residues: 904 sheet: -1.68 (0.31), residues: 253 loop : -1.27 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 417 TYR 0.040 0.003 TYR A 459 PHE 0.030 0.003 PHE A1172 TRP 0.069 0.004 TRP A1199 HIS 0.017 0.002 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00772 (16610) covalent geometry : angle 0.94191 (22451) hydrogen bonds : bond 0.14046 ( 897) hydrogen bonds : angle 6.80186 ( 2559) metal coordination : bond 0.31524 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.511 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 128 ILE cc_start: 0.6307 (mt) cc_final: 0.6001 (mt) REVERT: A 353 ILE cc_start: 0.4874 (mt) cc_final: 0.4631 (mt) REVERT: A 1215 MET cc_start: 0.3466 (mmp) cc_final: 0.3018 (mmp) REVERT: B 215 MET cc_start: 0.3171 (mmm) cc_final: 0.2721 (mmm) REVERT: B 218 MET cc_start: 0.6029 (tmm) cc_final: 0.5677 (mmm) REVERT: C 36 PRO cc_start: 0.7577 (Cg_endo) cc_final: 0.7264 (Cg_endo) REVERT: C 136 ASP cc_start: 0.7949 (m-30) cc_final: 0.7589 (p0) REVERT: C 145 ILE cc_start: 0.6205 (mt) cc_final: 0.5890 (mt) REVERT: C 439 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6424 (mm-40) REVERT: C 447 LEU cc_start: 0.6470 (mp) cc_final: 0.6005 (mt) REVERT: D 158 GLU cc_start: 0.8107 (tt0) cc_final: 0.7478 (tp30) REVERT: D 162 TYR cc_start: 0.6865 (m-10) cc_final: 0.6276 (m-80) outliers start: 1 outliers final: 1 residues processed: 474 average time/residue: 0.1464 time to fit residues: 98.1948 Evaluate side-chains 249 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 310 GLN A 387 GLN A 501 GLN A 592 HIS ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 ASN A1005 HIS A1092 GLN ** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 278 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.116014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.100746 restraints weight = 85082.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.102822 restraints weight = 54115.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.104039 restraints weight = 38062.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.104982 restraints weight = 29802.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.105592 restraints weight = 24803.893| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16612 Z= 0.178 Angle : 0.786 12.091 22451 Z= 0.397 Chirality : 0.047 0.222 2501 Planarity : 0.005 0.065 2857 Dihedral : 6.636 91.835 2182 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.62 % Allowed : 12.48 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.43 (0.19), residues: 1964 helix: 0.72 (0.16), residues: 912 sheet: -1.47 (0.32), residues: 263 loop : -0.95 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 296 TYR 0.039 0.002 TYR C 327 PHE 0.040 0.003 PHE C 377 TRP 0.032 0.002 TRP C 94 HIS 0.013 0.002 HIS A1102 Details of bonding type rmsd covalent geometry : bond 0.00392 (16610) covalent geometry : angle 0.78645 (22451) hydrogen bonds : bond 0.05173 ( 897) hydrogen bonds : angle 5.58453 ( 2559) metal coordination : bond 0.00928 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.571 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: A 239 MET cc_start: 0.6704 (mtt) cc_final: 0.6487 (mtt) REVERT: A 396 LEU cc_start: 0.8413 (pp) cc_final: 0.7799 (tt) REVERT: A 400 GLU cc_start: 0.5406 (tp30) cc_final: 0.5063 (tp30) REVERT: A 594 ARG cc_start: 0.7054 (mtm180) cc_final: 0.5645 (ttp-170) REVERT: A 992 HIS cc_start: 0.5810 (m-70) cc_final: 0.5142 (m-70) REVERT: A 1036 LEU cc_start: 0.8583 (tp) cc_final: 0.8297 (mt) REVERT: B 78 TYR cc_start: 0.7307 (t80) cc_final: 0.6929 (t80) REVERT: B 215 MET cc_start: 0.2665 (mmm) cc_final: 0.2236 (mmm) REVERT: C 35 LEU cc_start: 0.7815 (mp) cc_final: 0.7322 (tp) REVERT: C 136 ASP cc_start: 0.8326 (m-30) cc_final: 0.7636 (p0) REVERT: C 423 ASP cc_start: 0.8790 (t0) cc_final: 0.8272 (m-30) REVERT: D 111 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.6162 (t0) REVERT: D 158 GLU cc_start: 0.8616 (tt0) cc_final: 0.7993 (tp30) REVERT: D 162 TYR cc_start: 0.7589 (m-10) cc_final: 0.6957 (m-80) REVERT: D 167 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.4542 (mm-30) REVERT: D 254 MET cc_start: 0.8859 (tmm) cc_final: 0.8389 (tmm) outliers start: 47 outliers final: 21 residues processed: 308 average time/residue: 0.1324 time to fit residues: 58.9888 Evaluate side-chains 239 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 167 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 184 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 387 GLN A 501 GLN A 592 HIS ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN C 241 GLN D 258 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.113772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.097928 restraints weight = 85781.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.099978 restraints weight = 53728.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.101322 restraints weight = 37944.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.102232 restraints weight = 29312.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.102832 restraints weight = 24335.233| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16612 Z= 0.175 Angle : 0.724 10.215 22451 Z= 0.367 Chirality : 0.045 0.178 2501 Planarity : 0.005 0.046 2857 Dihedral : 6.126 74.119 2180 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.34 % Allowed : 14.99 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.22 (0.19), residues: 1964 helix: 0.89 (0.16), residues: 925 sheet: -1.33 (0.32), residues: 268 loop : -0.87 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 594 TYR 0.030 0.002 TYR C 327 PHE 0.036 0.002 PHE D 31 TRP 0.029 0.002 TRP D 438 HIS 0.013 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00384 (16610) covalent geometry : angle 0.72401 (22451) hydrogen bonds : bond 0.04674 ( 897) hydrogen bonds : angle 5.31865 ( 2559) metal coordination : bond 0.00088 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 0.678 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: A 327 TYR cc_start: 0.6084 (t80) cc_final: 0.5877 (t80) REVERT: A 396 LEU cc_start: 0.8574 (pp) cc_final: 0.8020 (tt) REVERT: A 594 ARG cc_start: 0.7168 (mtm180) cc_final: 0.6350 (ttp-170) REVERT: A 1020 TRP cc_start: 0.8200 (m100) cc_final: 0.7839 (m100) REVERT: A 1101 MET cc_start: 0.8549 (tpp) cc_final: 0.7112 (mtt) REVERT: A 1263 MET cc_start: 0.5504 (mtt) cc_final: 0.5227 (mtt) REVERT: B 85 TRP cc_start: 0.6070 (m-10) cc_final: 0.5747 (m-10) REVERT: B 215 MET cc_start: 0.2808 (mmm) cc_final: 0.2429 (mmm) REVERT: B 218 MET cc_start: 0.6900 (mmm) cc_final: 0.6553 (mmp) REVERT: C 35 LEU cc_start: 0.7806 (mp) cc_final: 0.7413 (tp) REVERT: C 136 ASP cc_start: 0.8283 (m-30) cc_final: 0.7754 (p0) REVERT: C 293 LEU cc_start: 0.6361 (tp) cc_final: 0.6160 (tp) REVERT: C 332 ASP cc_start: 0.6492 (OUTLIER) cc_final: 0.5778 (p0) REVERT: C 404 THR cc_start: 0.7416 (p) cc_final: 0.7165 (t) REVERT: C 423 ASP cc_start: 0.8813 (t0) cc_final: 0.8264 (m-30) REVERT: C 447 LEU cc_start: 0.7867 (mp) cc_final: 0.6895 (tp) REVERT: D 158 GLU cc_start: 0.8787 (tt0) cc_final: 0.8202 (tp30) REVERT: D 162 TYR cc_start: 0.7846 (m-10) cc_final: 0.7245 (m-80) REVERT: D 254 MET cc_start: 0.8651 (tmm) cc_final: 0.8433 (tmm) outliers start: 60 outliers final: 30 residues processed: 280 average time/residue: 0.1280 time to fit residues: 53.3641 Evaluate side-chains 235 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 188 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS A 501 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS A 621 GLN A 705 GLN ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 270 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.113111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.098107 restraints weight = 85625.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.100111 restraints weight = 54721.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.101341 restraints weight = 38674.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.102220 restraints weight = 30248.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.102807 restraints weight = 25259.533| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16612 Z= 0.162 Angle : 0.692 8.879 22451 Z= 0.350 Chirality : 0.044 0.192 2501 Planarity : 0.004 0.047 2857 Dihedral : 5.885 74.802 2180 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.23 % Allowed : 16.77 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.02 (0.19), residues: 1964 helix: 1.08 (0.16), residues: 920 sheet: -1.35 (0.31), residues: 267 loop : -0.75 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 145 TYR 0.026 0.002 TYR C 327 PHE 0.031 0.002 PHE D 31 TRP 0.020 0.002 TRP D 438 HIS 0.013 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00357 (16610) covalent geometry : angle 0.69164 (22451) hydrogen bonds : bond 0.04380 ( 897) hydrogen bonds : angle 5.12993 ( 2559) metal coordination : bond 0.00272 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 0.444 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: A 396 LEU cc_start: 0.8574 (pp) cc_final: 0.7902 (tt) REVERT: A 594 ARG cc_start: 0.7102 (mtm180) cc_final: 0.6269 (ttp-110) REVERT: A 1020 TRP cc_start: 0.8287 (m100) cc_final: 0.7866 (m100) REVERT: A 1263 MET cc_start: 0.5509 (mtt) cc_final: 0.5180 (mtt) REVERT: B 85 TRP cc_start: 0.5774 (m-10) cc_final: 0.5517 (m-10) REVERT: B 171 GLN cc_start: 0.3343 (OUTLIER) cc_final: 0.2998 (pp30) REVERT: B 215 MET cc_start: 0.2835 (mmm) cc_final: 0.2479 (mmm) REVERT: B 218 MET cc_start: 0.6668 (mmm) cc_final: 0.6377 (mmp) REVERT: C 35 LEU cc_start: 0.7723 (mp) cc_final: 0.7406 (tp) REVERT: C 332 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.5643 (p0) REVERT: C 423 ASP cc_start: 0.8808 (t0) cc_final: 0.8285 (m-30) REVERT: D 158 GLU cc_start: 0.8678 (tt0) cc_final: 0.8161 (tp30) REVERT: D 162 TYR cc_start: 0.7779 (m-10) cc_final: 0.7211 (m-80) REVERT: D 167 GLU cc_start: 0.6486 (mp0) cc_final: 0.4442 (mm-30) REVERT: D 435 ASN cc_start: 0.9154 (m110) cc_final: 0.8798 (m110) outliers start: 58 outliers final: 31 residues processed: 270 average time/residue: 0.1074 time to fit residues: 44.6438 Evaluate side-chains 237 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 67 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 160 ASN A 352 ASN A 501 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 141 HIS D 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.113615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.098520 restraints weight = 85217.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.100530 restraints weight = 54991.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.101824 restraints weight = 39282.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.102662 restraints weight = 30790.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.103244 restraints weight = 25841.740| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16612 Z= 0.140 Angle : 0.664 10.772 22451 Z= 0.335 Chirality : 0.044 0.346 2501 Planarity : 0.004 0.058 2857 Dihedral : 5.701 75.727 2180 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 18.33 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1964 helix: 1.24 (0.17), residues: 926 sheet: -1.19 (0.32), residues: 260 loop : -0.74 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.025 0.001 TYR A 327 PHE 0.027 0.002 PHE D 31 TRP 0.027 0.002 TRP A 127 HIS 0.009 0.001 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.00311 (16610) covalent geometry : angle 0.66399 (22451) hydrogen bonds : bond 0.04141 ( 897) hydrogen bonds : angle 5.01932 ( 2559) metal coordination : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.733 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: A 396 LEU cc_start: 0.8631 (pp) cc_final: 0.7992 (tt) REVERT: A 594 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6610 (mtm180) REVERT: A 1020 TRP cc_start: 0.8151 (m100) cc_final: 0.7873 (m100) REVERT: A 1101 MET cc_start: 0.8644 (mmm) cc_final: 0.6211 (mtt) REVERT: A 1263 MET cc_start: 0.5648 (mtt) cc_final: 0.5204 (mtt) REVERT: B 85 TRP cc_start: 0.5889 (m-10) cc_final: 0.5624 (m-10) REVERT: B 215 MET cc_start: 0.2775 (mmm) cc_final: 0.2435 (mmm) REVERT: C 332 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.5743 (p0) REVERT: C 382 LEU cc_start: 0.8328 (mp) cc_final: 0.7818 (tp) REVERT: C 423 ASP cc_start: 0.8786 (t0) cc_final: 0.8270 (m-30) REVERT: C 427 TYR cc_start: 0.8248 (t80) cc_final: 0.7570 (t80) REVERT: D 158 GLU cc_start: 0.8625 (tt0) cc_final: 0.8155 (tp30) REVERT: D 162 TYR cc_start: 0.7763 (m-10) cc_final: 0.7339 (m-80) REVERT: D 167 GLU cc_start: 0.6488 (mt-10) cc_final: 0.4515 (mm-30) outliers start: 52 outliers final: 30 residues processed: 260 average time/residue: 0.1086 time to fit residues: 43.9879 Evaluate side-chains 229 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 149 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN A 592 HIS A 705 GLN ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 270 HIS D 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.112745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.097949 restraints weight = 85911.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.099880 restraints weight = 54494.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.101181 restraints weight = 38969.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.102032 restraints weight = 30274.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.102594 restraints weight = 25323.631| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16612 Z= 0.143 Angle : 0.672 10.286 22451 Z= 0.335 Chirality : 0.043 0.219 2501 Planarity : 0.004 0.068 2857 Dihedral : 5.637 74.485 2180 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.67 % Allowed : 18.83 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.23 (0.19), residues: 1964 helix: 1.31 (0.17), residues: 927 sheet: -1.20 (0.32), residues: 260 loop : -0.70 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 145 TYR 0.023 0.001 TYR A 327 PHE 0.031 0.002 PHE A 259 TRP 0.035 0.002 TRP A 127 HIS 0.010 0.001 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.00320 (16610) covalent geometry : angle 0.67174 (22451) hydrogen bonds : bond 0.04107 ( 897) hydrogen bonds : angle 4.97645 ( 2559) metal coordination : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.551 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: A 396 LEU cc_start: 0.8605 (pp) cc_final: 0.8000 (tt) REVERT: A 453 ARG cc_start: 0.6838 (tpt170) cc_final: 0.6567 (tpt170) REVERT: A 563 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8147 (mmp80) REVERT: A 594 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6295 (ttp-110) REVERT: A 1019 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 1263 MET cc_start: 0.5642 (mtt) cc_final: 0.5180 (mtt) REVERT: B 85 TRP cc_start: 0.5913 (m-10) cc_final: 0.5664 (m-10) REVERT: C 382 LEU cc_start: 0.8298 (mp) cc_final: 0.7774 (tp) REVERT: C 396 LYS cc_start: 0.7347 (mmtm) cc_final: 0.7127 (tppt) REVERT: C 423 ASP cc_start: 0.8758 (t0) cc_final: 0.8224 (m-30) REVERT: D 158 GLU cc_start: 0.8629 (tt0) cc_final: 0.8170 (tp30) REVERT: D 162 TYR cc_start: 0.7830 (m-10) cc_final: 0.7287 (m-80) REVERT: D 167 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6221 (pt0) outliers start: 48 outliers final: 33 residues processed: 245 average time/residue: 0.1156 time to fit residues: 43.9286 Evaluate side-chains 235 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 84 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 153 ASN A 373 ASN A 501 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 HIS B 171 GLN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.107935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.093619 restraints weight = 88433.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.095538 restraints weight = 56298.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.096708 restraints weight = 40059.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.097544 restraints weight = 31461.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.098051 restraints weight = 26431.713| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16612 Z= 0.261 Angle : 0.819 15.066 22451 Z= 0.417 Chirality : 0.048 0.179 2501 Planarity : 0.005 0.075 2857 Dihedral : 6.064 75.308 2180 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.68 % Allowed : 18.55 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.27 (0.18), residues: 1964 helix: 0.81 (0.16), residues: 921 sheet: -1.24 (0.31), residues: 264 loop : -0.89 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 312 TYR 0.020 0.002 TYR A 702 PHE 0.026 0.003 PHE D 325 TRP 0.042 0.003 TRP A 127 HIS 0.027 0.002 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00572 (16610) covalent geometry : angle 0.81908 (22451) hydrogen bonds : bond 0.04859 ( 897) hydrogen bonds : angle 5.34755 ( 2559) metal coordination : bond 0.00565 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 0.668 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: A 396 LEU cc_start: 0.8557 (pp) cc_final: 0.7904 (tt) REVERT: A 453 ARG cc_start: 0.6676 (tpt170) cc_final: 0.6472 (tpt170) REVERT: A 594 ARG cc_start: 0.7365 (mtm180) cc_final: 0.6665 (ttp-110) REVERT: A 1019 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 1020 TRP cc_start: 0.8045 (m100) cc_final: 0.7744 (m100) REVERT: A 1101 MET cc_start: 0.8716 (mmm) cc_final: 0.6526 (mtt) REVERT: A 1263 MET cc_start: 0.6001 (mtt) cc_final: 0.5576 (mtt) REVERT: B 171 GLN cc_start: 0.3765 (OUTLIER) cc_final: 0.3560 (pp30) REVERT: D 158 GLU cc_start: 0.8613 (tt0) cc_final: 0.7965 (tp30) REVERT: D 162 TYR cc_start: 0.7621 (m-10) cc_final: 0.6990 (m-80) REVERT: D 442 TRP cc_start: 0.7065 (t60) cc_final: 0.5859 (t60) outliers start: 66 outliers final: 46 residues processed: 248 average time/residue: 0.1067 time to fit residues: 41.1525 Evaluate side-chains 240 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1212 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain B residue 35 TYR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 TRP Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 174 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 160 ASN A 501 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 HIS ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN D 40 GLN D 258 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.110797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.096402 restraints weight = 87743.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.098487 restraints weight = 54378.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.099677 restraints weight = 38076.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.100635 restraints weight = 29472.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.101216 restraints weight = 24453.639| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16612 Z= 0.149 Angle : 0.722 12.217 22451 Z= 0.356 Chirality : 0.044 0.179 2501 Planarity : 0.005 0.076 2857 Dihedral : 5.774 70.788 2180 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.73 % Allowed : 19.89 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.08 (0.19), residues: 1964 helix: 1.19 (0.17), residues: 925 sheet: -1.16 (0.32), residues: 243 loop : -0.83 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 672 TYR 0.019 0.002 TYR C 327 PHE 0.030 0.002 PHE A 259 TRP 0.031 0.002 TRP A 127 HIS 0.011 0.001 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.00334 (16610) covalent geometry : angle 0.72198 (22451) hydrogen bonds : bond 0.04242 ( 897) hydrogen bonds : angle 5.05618 ( 2559) metal coordination : bond 0.00210 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.608 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: A 101 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6783 (mt) REVERT: A 396 LEU cc_start: 0.8529 (pp) cc_final: 0.7939 (tt) REVERT: A 594 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6485 (ttp-110) REVERT: A 642 MET cc_start: 0.6112 (mmt) cc_final: 0.5467 (mmp) REVERT: A 1020 TRP cc_start: 0.7964 (m100) cc_final: 0.7594 (m100) REVERT: A 1101 MET cc_start: 0.8712 (mmm) cc_final: 0.6397 (mtt) REVERT: A 1263 MET cc_start: 0.5854 (mtt) cc_final: 0.5515 (mtt) REVERT: B 140 MET cc_start: 0.7737 (tmm) cc_final: 0.7445 (tpp) REVERT: B 215 MET cc_start: 0.3181 (mmm) cc_final: 0.2953 (mmt) REVERT: C 82 ARG cc_start: 0.7087 (mmt-90) cc_final: 0.6841 (mmt-90) REVERT: C 396 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7309 (tppt) REVERT: C 423 ASP cc_start: 0.8737 (t0) cc_final: 0.8199 (m-30) REVERT: D 133 ASP cc_start: 0.7612 (p0) cc_final: 0.7299 (p0) REVERT: D 158 GLU cc_start: 0.8409 (tt0) cc_final: 0.7705 (tp30) REVERT: D 162 TYR cc_start: 0.7587 (m-10) cc_final: 0.6609 (m-80) REVERT: D 442 TRP cc_start: 0.6984 (t60) cc_final: 0.6635 (t60) outliers start: 49 outliers final: 33 residues processed: 236 average time/residue: 0.1068 time to fit residues: 39.6090 Evaluate side-chains 226 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 147 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 96 optimal weight: 0.0570 chunk 126 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 501 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 241 GLN C 249 ASN C 430 ASN D 40 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.106085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.091754 restraints weight = 89262.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.093653 restraints weight = 56695.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.094822 restraints weight = 40472.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.095641 restraints weight = 31950.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.096161 restraints weight = 26901.714| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 16612 Z= 0.299 Angle : 0.882 14.171 22451 Z= 0.445 Chirality : 0.050 0.237 2501 Planarity : 0.006 0.078 2857 Dihedral : 6.298 71.476 2180 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.06 % Allowed : 20.22 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.52 (0.18), residues: 1964 helix: 0.67 (0.16), residues: 926 sheet: -1.48 (0.31), residues: 257 loop : -1.08 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 417 TYR 0.029 0.002 TYR A 673 PHE 0.034 0.003 PHE A 259 TRP 0.041 0.003 TRP A 127 HIS 0.015 0.002 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00662 (16610) covalent geometry : angle 0.88206 (22451) hydrogen bonds : bond 0.05111 ( 897) hydrogen bonds : angle 5.55554 ( 2559) metal coordination : bond 0.00208 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.603 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: A 240 ASP cc_start: 0.8299 (m-30) cc_final: 0.7721 (t0) REVERT: A 396 LEU cc_start: 0.8589 (pp) cc_final: 0.8021 (tt) REVERT: A 417 ARG cc_start: 0.7268 (ptp90) cc_final: 0.6863 (ptp90) REVERT: A 592 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5880 (m170) REVERT: A 594 ARG cc_start: 0.7533 (mtm180) cc_final: 0.7018 (mtm-85) REVERT: A 1020 TRP cc_start: 0.8036 (m100) cc_final: 0.7621 (m100) REVERT: A 1040 ARG cc_start: 0.3759 (mtt180) cc_final: 0.3185 (ttt-90) REVERT: A 1101 MET cc_start: 0.8710 (mmm) cc_final: 0.6676 (mtt) REVERT: A 1263 MET cc_start: 0.6216 (mtt) cc_final: 0.5821 (mtt) REVERT: B 215 MET cc_start: 0.3956 (mmm) cc_final: 0.3714 (mmt) REVERT: C 420 LEU cc_start: 0.8553 (tt) cc_final: 0.8236 (tp) REVERT: D 158 GLU cc_start: 0.8582 (tt0) cc_final: 0.7748 (tp30) REVERT: D 162 TYR cc_start: 0.7727 (m-10) cc_final: 0.7035 (m-80) REVERT: D 442 TRP cc_start: 0.7140 (t60) cc_final: 0.6754 (t60) outliers start: 55 outliers final: 48 residues processed: 237 average time/residue: 0.0979 time to fit residues: 36.9094 Evaluate side-chains 242 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1212 MET Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 49 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 138 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 197 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN A 592 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN D 19 GLN D 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.111035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.096870 restraints weight = 88169.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.098958 restraints weight = 54698.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.100273 restraints weight = 38093.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.101145 restraints weight = 29414.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.101715 restraints weight = 24370.882| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16612 Z= 0.145 Angle : 0.761 14.574 22451 Z= 0.371 Chirality : 0.046 0.255 2501 Planarity : 0.005 0.081 2857 Dihedral : 5.834 66.174 2180 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.06 % Allowed : 21.56 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.05 (0.18), residues: 1964 helix: 1.08 (0.17), residues: 914 sheet: -1.17 (0.32), residues: 234 loop : -0.90 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.023 0.002 TYR A 673 PHE 0.023 0.002 PHE A 678 TRP 0.030 0.002 TRP A 127 HIS 0.012 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00316 (16610) covalent geometry : angle 0.76084 (22451) hydrogen bonds : bond 0.04354 ( 897) hydrogen bonds : angle 5.08388 ( 2559) metal coordination : bond 0.00370 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.624 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: A 101 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6799 (mt) REVERT: A 175 LEU cc_start: 0.6846 (mm) cc_final: 0.6236 (mm) REVERT: A 259 PHE cc_start: 0.6083 (m-80) cc_final: 0.5769 (m-10) REVERT: A 396 LEU cc_start: 0.8462 (pp) cc_final: 0.7925 (tt) REVERT: A 417 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6629 (ptp90) REVERT: A 594 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6971 (mtm180) REVERT: A 642 MET cc_start: 0.6014 (mmt) cc_final: 0.5272 (mmp) REVERT: A 779 MET cc_start: 0.7185 (mpp) cc_final: 0.6900 (mtt) REVERT: A 1020 TRP cc_start: 0.7917 (m100) cc_final: 0.7654 (m100) REVERT: A 1040 ARG cc_start: 0.3696 (mtt180) cc_final: 0.3182 (ttt-90) REVERT: A 1101 MET cc_start: 0.8723 (mmm) cc_final: 0.6725 (mtt) REVERT: A 1212 MET cc_start: 0.3530 (OUTLIER) cc_final: 0.3217 (tmm) REVERT: A 1263 MET cc_start: 0.6209 (mtt) cc_final: 0.5910 (mtt) REVERT: C 82 ARG cc_start: 0.7108 (mmt-90) cc_final: 0.6666 (mmp80) REVERT: C 396 LYS cc_start: 0.7643 (mmtm) cc_final: 0.7331 (tppt) REVERT: C 423 ASP cc_start: 0.8750 (t0) cc_final: 0.8322 (m-30) REVERT: D 158 GLU cc_start: 0.8376 (tt0) cc_final: 0.7524 (tp30) REVERT: D 162 TYR cc_start: 0.7525 (m-10) cc_final: 0.6649 (m-80) REVERT: D 330 LEU cc_start: 0.6846 (pp) cc_final: 0.6114 (mm) REVERT: D 442 TRP cc_start: 0.6922 (t60) cc_final: 0.6601 (t60) outliers start: 37 outliers final: 31 residues processed: 233 average time/residue: 0.1122 time to fit residues: 40.5282 Evaluate side-chains 228 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1212 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1243 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 94 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 53 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 48 optimal weight: 0.0060 chunk 94 optimal weight: 0.0270 chunk 80 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 485 ASN A 501 GLN A 592 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.111359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.097319 restraints weight = 88157.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.099345 restraints weight = 54773.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.100662 restraints weight = 38433.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.101529 restraints weight = 29687.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.102101 restraints weight = 24587.968| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16612 Z= 0.142 Angle : 0.760 15.442 22451 Z= 0.368 Chirality : 0.046 0.299 2501 Planarity : 0.005 0.080 2857 Dihedral : 5.647 63.096 2180 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.12 % Allowed : 21.78 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.11 (0.19), residues: 1964 helix: 1.16 (0.17), residues: 919 sheet: -1.09 (0.33), residues: 234 loop : -0.77 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 594 TYR 0.030 0.002 TYR A 673 PHE 0.021 0.002 PHE D 288 TRP 0.030 0.002 TRP A 127 HIS 0.014 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00315 (16610) covalent geometry : angle 0.75965 (22451) hydrogen bonds : bond 0.04253 ( 897) hydrogen bonds : angle 4.98794 ( 2559) metal coordination : bond 0.00150 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.78 seconds wall clock time: 53 minutes 31.78 seconds (3211.78 seconds total)