Starting phenix.real_space_refine on Sat Aug 23 07:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cde_16570/08_2025/8cde_16570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cde_16570/08_2025/8cde_16570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cde_16570/08_2025/8cde_16570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cde_16570/08_2025/8cde_16570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cde_16570/08_2025/8cde_16570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cde_16570/08_2025/8cde_16570.map" } resolution = 3.1 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= 0.007 sd= 1.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 6608 2.51 5 N 1736 2.21 5 O 2044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4785 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 575} Chain breaks: 2 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2559 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 4 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1568 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Time building chain proxies: 2.04, per 1000 atoms: 0.19 Number of scatterers: 10464 At special positions: 0 Unit cell: (87.36, 120.64, 148.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2044 8.00 N 1736 7.00 C 6608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 637 " distance=2.03 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 625 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 659 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 691 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 703 " - pdb=" SG CYS A 714 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 268 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 152 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 123 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 228 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 268.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 32 sheets defined 9.9% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.754A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.655A pdb=" N LYS A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.156A pdb=" N ILE A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.773A pdb=" N THR A 623 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.640A pdb=" N SER A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 removed outlier: 3.674A pdb=" N GLU C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 217 through 223 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 74 removed outlier: 3.599A pdb=" N TYR A 68 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 150 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE A 72 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 148 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.991A pdb=" N GLN A 243 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU A 187 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 245 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE A 185 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 192 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 312 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS B 303 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER B 293 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 179 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.560A pdb=" N THR A 336 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 349 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.549A pdb=" N LEU A 473 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 409 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL A 475 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE A 407 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 391 removed outlier: 5.734A pdb=" N CYS A 474 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 381 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N ILE A 560 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS A 637 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 630 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A 588 " --> pdb=" O TYR A 630 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A 632 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 586 " --> pdb=" O PHE A 632 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER A 634 " --> pdb=" O ASP A 584 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AB5, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AB6, first strand: chain 'A' and resid 689 through 693 Processing sheet with id=AB7, first strand: chain 'A' and resid 708 through 710 Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 43 removed outlier: 3.559A pdb=" N ASN B 352 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 341 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS B 334 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE B 343 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE B 332 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 56 removed outlier: 5.280A pdb=" N LEU B 60 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 91 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS B 81 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR B 89 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.632A pdb=" N ALA B 147 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 135 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 169 through 171 removed outlier: 3.569A pdb=" N PHE B 177 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 196 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS B 268 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B 237 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.939A pdb=" N PHE B 226 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AC5, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.332A pdb=" N VAL C 30 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 102 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP C 52 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 63 " --> pdb=" O GLN C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.332A pdb=" N VAL C 30 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 102 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 108 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.079A pdb=" N TYR C 191 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AC9, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.628A pdb=" N ARG D 99 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.938A pdb=" N ILE D 142 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET D 54 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER D 70 " --> pdb=" O MET D 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP D 56 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.938A pdb=" N ILE D 142 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N CYS D 115 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP D 135 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS D 117 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 168 through 177 removed outlier: 5.703A pdb=" N TYR D 208 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 168 through 177 removed outlier: 5.703A pdb=" N TYR D 208 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 183 through 186 removed outlier: 3.715A pdb=" N THR D 183 " --> pdb=" O ASN D 231 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3369 1.34 - 1.46: 2561 1.46 - 1.58: 4668 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 10683 Sorted by residual: bond pdb=" CB LYS D 233 " pdb=" CG LYS D 233 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CA ASP D 176 " pdb=" CB ASP D 176 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.63e+00 bond pdb=" CB GLU C 161 " pdb=" CG GLU C 161 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CG LYS D 233 " pdb=" CD LYS D 233 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 14267 2.78 - 5.56: 149 5.56 - 8.33: 21 8.33 - 11.11: 1 11.11 - 13.89: 1 Bond angle restraints: 14439 Sorted by residual: angle pdb=" CB MET B 131 " pdb=" CG MET B 131 " pdb=" SD MET B 131 " ideal model delta sigma weight residual 112.70 126.59 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C LYS D 175 " pdb=" N ASP D 176 " pdb=" CA ASP D 176 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" CA LYS A 49 " pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA TYR A 286 " pdb=" CB TYR A 286 " pdb=" CG TYR A 286 " ideal model delta sigma weight residual 113.90 120.05 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CB LYS D 233 " pdb=" CG LYS D 233 " pdb=" CD LYS D 233 " ideal model delta sigma weight residual 111.30 118.91 -7.61 2.30e+00 1.89e-01 1.10e+01 ... (remaining 14434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5566 17.72 - 35.45: 696 35.45 - 53.17: 177 53.17 - 70.89: 34 70.89 - 88.62: 10 Dihedral angle restraints: 6483 sinusoidal: 2621 harmonic: 3862 Sorted by residual: dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual -86.00 -155.54 69.54 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS B 48 " pdb=" SG CYS B 48 " pdb=" SG CYS B 64 " pdb=" CB CYS B 64 " ideal model delta sinusoidal sigma weight residual 93.00 147.44 -54.44 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 133 " pdb=" CB CYS B 133 " ideal model delta sinusoidal sigma weight residual 93.00 41.30 51.70 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 6480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1200 0.049 - 0.097: 287 0.097 - 0.146: 88 0.146 - 0.195: 2 0.195 - 0.243: 1 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA ASP D 176 " pdb=" N ASP D 176 " pdb=" C ASP D 176 " pdb=" CB ASP D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA TYR A 286 " pdb=" N TYR A 286 " pdb=" C TYR A 286 " pdb=" CB TYR A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA ILE A 122 " pdb=" N ILE A 122 " pdb=" C ILE A 122 " pdb=" CB ILE A 122 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1575 not shown) Planarity restraints: 1859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 218 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ASN B 218 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 218 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR B 219 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 322 " -0.009 2.00e-02 2.50e+03 1.30e-02 3.37e+00 pdb=" CG TYR A 322 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 322 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 322 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 322 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 322 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 322 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 287 " 0.136 9.50e-02 1.11e+02 6.15e-02 2.96e+00 pdb=" NE ARG A 287 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 287 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 287 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 287 " 0.000 2.00e-02 2.50e+03 ... (remaining 1856 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 338 2.68 - 3.24: 10302 3.24 - 3.79: 15786 3.79 - 4.35: 21649 4.35 - 4.90: 35338 Nonbonded interactions: 83413 Sorted by model distance: nonbonded pdb=" OH TYR C 53 " pdb=" O VAL D 129 " model vdw 2.129 3.040 nonbonded pdb=" OE1 GLU C 101 " pdb=" OH TYR C 191 " model vdw 2.211 3.040 nonbonded pdb=" N GLU C 141 " pdb=" OE1 GLU C 141 " model vdw 2.230 3.120 nonbonded pdb=" O VAL A 295 " pdb=" NZ LYS A 309 " model vdw 2.231 3.120 nonbonded pdb=" O ALA A 586 " pdb=" OG1 THR A 600 " model vdw 2.250 3.040 ... (remaining 83408 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 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: 9.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.003 0.040 10716 Z= 0.128 Angle : 0.715 13.889 14505 Z= 0.368 Chirality : 0.045 0.243 1578 Planarity : 0.004 0.062 1859 Dihedral : 16.552 88.618 3910 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.94 % Allowed : 27.41 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.23), residues: 1295 helix: -1.20 (0.54), residues: 84 sheet: -0.60 (0.25), residues: 449 loop : -1.65 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 339 TYR 0.026 0.001 TYR A 286 PHE 0.013 0.001 PHE B 307 TRP 0.014 0.001 TRP B 87 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00290 (10683) covalent geometry : angle 0.71399 (14439) SS BOND : bond 0.00246 ( 33) SS BOND : angle 0.90627 ( 66) hydrogen bonds : bond 0.25471 ( 333) hydrogen bonds : angle 9.46909 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8571 (mmtt) REVERT: B 236 ASP cc_start: 0.7540 (m-30) cc_final: 0.7317 (p0) REVERT: B 276 ASP cc_start: 0.8624 (m-30) cc_final: 0.8328 (p0) REVERT: B 358 TYR cc_start: 0.7614 (t80) cc_final: 0.7347 (t80) REVERT: C 49 TYR cc_start: 0.8419 (m-10) cc_final: 0.8158 (m-10) REVERT: C 72 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8335 (ttp80) REVERT: C 101 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7708 (mm-30) REVERT: C 160 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7371 (ttm-80) REVERT: C 187 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9146 (mmmm) REVERT: D 31 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8036 (mm110) REVERT: D 63 LYS cc_start: 0.6638 (tptp) cc_final: 0.6336 (tptp) REVERT: D 140 GLU cc_start: 0.7288 (pp20) cc_final: 0.6913 (pp20) outliers start: 47 outliers final: 32 residues processed: 168 average time/residue: 0.0952 time to fit residues: 22.3144 Evaluate side-chains 139 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 185 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 280 ASN A 358 ASN A 459 ASN B 134 HIS B 139 ASN B 191 ASN B 240 HIS B 308 ASN B 352 ASN C 70 GLN C 217 GLN D 59 GLN D 203 GLN D 232 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.111049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.086992 restraints weight = 29453.534| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.50 r_work: 0.3566 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10716 Z= 0.142 Angle : 0.638 9.339 14505 Z= 0.337 Chirality : 0.045 0.178 1578 Planarity : 0.004 0.045 1859 Dihedral : 6.975 56.241 1469 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.69 % Allowed : 23.55 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.23), residues: 1295 helix: -1.05 (0.55), residues: 81 sheet: -0.29 (0.25), residues: 450 loop : -1.48 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.016 0.001 TYR A 286 PHE 0.016 0.001 PHE A 221 TRP 0.008 0.001 TRP D 67 HIS 0.004 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00314 (10683) covalent geometry : angle 0.63731 (14439) SS BOND : bond 0.00398 ( 33) SS BOND : angle 0.85664 ( 66) hydrogen bonds : bond 0.03976 ( 333) hydrogen bonds : angle 6.70842 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8100 (ttp80) REVERT: A 435 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8298 (mmtt) REVERT: A 564 GLU cc_start: 0.8126 (mp0) cc_final: 0.7780 (mp0) REVERT: B 236 ASP cc_start: 0.7638 (m-30) cc_final: 0.7367 (p0) REVERT: B 276 ASP cc_start: 0.8865 (m-30) cc_final: 0.8510 (p0) REVERT: B 334 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8607 (tptp) REVERT: B 336 ASP cc_start: 0.8078 (t0) cc_final: 0.7780 (t0) REVERT: C 72 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8557 (ttp80) REVERT: C 109 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7119 (ttt90) REVERT: C 185 ASP cc_start: 0.7597 (t0) cc_final: 0.7383 (t0) REVERT: C 187 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9184 (mmmm) REVERT: C 193 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8092 (tt) REVERT: D 31 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8123 (mm110) REVERT: D 63 LYS cc_start: 0.6694 (tptp) cc_final: 0.6329 (tptp) REVERT: D 140 GLU cc_start: 0.7663 (pp20) cc_final: 0.7417 (pp20) REVERT: D 203 GLN cc_start: 0.7815 (mt0) cc_final: 0.7502 (mp10) outliers start: 56 outliers final: 29 residues processed: 173 average time/residue: 0.0922 time to fit residues: 22.5819 Evaluate side-chains 143 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.109679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.085819 restraints weight = 29703.067| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 4.46 r_work: 0.3542 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10716 Z= 0.148 Angle : 0.609 9.946 14505 Z= 0.321 Chirality : 0.045 0.214 1578 Planarity : 0.004 0.047 1859 Dihedral : 5.970 49.546 1447 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.20 % Allowed : 23.55 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.23), residues: 1295 helix: -0.99 (0.54), residues: 81 sheet: -0.21 (0.26), residues: 449 loop : -1.39 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 339 TYR 0.014 0.001 TYR C 53 PHE 0.033 0.001 PHE A 221 TRP 0.007 0.001 TRP C 52 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00331 (10683) covalent geometry : angle 0.60778 (14439) SS BOND : bond 0.00381 ( 33) SS BOND : angle 0.89446 ( 66) hydrogen bonds : bond 0.03553 ( 333) hydrogen bonds : angle 6.26409 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 113 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.7710 (mttt) cc_final: 0.7325 (ttmt) REVERT: A 287 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: A 435 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8343 (mmtt) REVERT: A 618 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 276 ASP cc_start: 0.8879 (m-30) cc_final: 0.8503 (p0) REVERT: C 72 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8590 (ttp80) REVERT: C 109 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7238 (ttt90) REVERT: C 185 ASP cc_start: 0.7772 (t0) cc_final: 0.7482 (t0) REVERT: C 187 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9208 (mmmm) REVERT: C 193 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8024 (tt) REVERT: D 31 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8118 (mm110) REVERT: D 63 LYS cc_start: 0.6544 (tptp) cc_final: 0.6222 (tptp) REVERT: D 140 GLU cc_start: 0.7712 (pp20) cc_final: 0.7471 (pp20) REVERT: D 195 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8158 (t) REVERT: D 203 GLN cc_start: 0.7850 (mt0) cc_final: 0.7638 (mp10) outliers start: 62 outliers final: 40 residues processed: 162 average time/residue: 0.0830 time to fit residues: 19.2008 Evaluate side-chains 147 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 88 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 78 optimal weight: 0.0270 chunk 41 optimal weight: 0.0170 chunk 127 optimal weight: 3.9990 overall best weight: 0.9836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 575 GLN D 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.108924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085129 restraints weight = 29782.047| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 4.44 r_work: 0.3528 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10716 Z= 0.162 Angle : 0.604 9.959 14505 Z= 0.317 Chirality : 0.044 0.175 1578 Planarity : 0.003 0.047 1859 Dihedral : 5.769 49.876 1439 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.11 % Allowed : 24.64 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.23), residues: 1295 helix: -0.92 (0.56), residues: 81 sheet: -0.22 (0.26), residues: 451 loop : -1.33 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 339 TYR 0.013 0.001 TYR C 53 PHE 0.035 0.001 PHE A 221 TRP 0.008 0.001 TRP C 52 HIS 0.003 0.001 HIS A 645 Details of bonding type rmsd covalent geometry : bond 0.00364 (10683) covalent geometry : angle 0.60245 (14439) SS BOND : bond 0.00366 ( 33) SS BOND : angle 0.90554 ( 66) hydrogen bonds : bond 0.03347 ( 333) hydrogen bonds : angle 6.09434 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 110 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8399 (mmtt) REVERT: B 131 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.6080 (ppp) REVERT: C 109 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7287 (ttt90) REVERT: C 185 ASP cc_start: 0.7767 (t0) cc_final: 0.7405 (t0) REVERT: C 187 LYS cc_start: 0.9479 (mmmm) cc_final: 0.9207 (mmmm) REVERT: C 193 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8052 (tt) REVERT: D 31 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8140 (mm110) REVERT: D 63 LYS cc_start: 0.6691 (tptp) cc_final: 0.6369 (tptp) REVERT: D 140 GLU cc_start: 0.7724 (pp20) cc_final: 0.7470 (pp20) REVERT: D 195 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8079 (t) outliers start: 61 outliers final: 39 residues processed: 160 average time/residue: 0.0927 time to fit residues: 21.0401 Evaluate side-chains 141 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.109667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086025 restraints weight = 29787.677| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.47 r_work: 0.3549 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10716 Z= 0.135 Angle : 0.598 10.124 14505 Z= 0.311 Chirality : 0.044 0.172 1578 Planarity : 0.003 0.047 1859 Dihedral : 5.610 49.159 1437 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.69 % Allowed : 25.48 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.23), residues: 1295 helix: -0.83 (0.57), residues: 80 sheet: -0.19 (0.26), residues: 449 loop : -1.32 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.012 0.001 TYR C 53 PHE 0.036 0.001 PHE A 221 TRP 0.007 0.001 TRP C 52 HIS 0.003 0.001 HIS A 645 Details of bonding type rmsd covalent geometry : bond 0.00303 (10683) covalent geometry : angle 0.59701 (14439) SS BOND : bond 0.00392 ( 33) SS BOND : angle 0.84115 ( 66) hydrogen bonds : bond 0.03158 ( 333) hydrogen bonds : angle 5.94121 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7922 (mtpp) REVERT: A 435 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8393 (mmtt) REVERT: A 567 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8570 (ttm170) REVERT: A 618 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8805 (tt) REVERT: A 654 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7690 (tpm170) REVERT: B 131 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6062 (ppp) REVERT: C 109 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7287 (ttt90) REVERT: C 185 ASP cc_start: 0.7814 (t0) cc_final: 0.7502 (t0) REVERT: C 187 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9178 (mmmm) REVERT: C 193 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8080 (tt) REVERT: D 31 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8168 (mm110) REVERT: D 63 LYS cc_start: 0.6643 (tptp) cc_final: 0.6355 (tptp) REVERT: D 140 GLU cc_start: 0.7697 (pp20) cc_final: 0.7465 (pp20) REVERT: D 195 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8062 (t) outliers start: 56 outliers final: 38 residues processed: 159 average time/residue: 0.1048 time to fit residues: 23.3257 Evaluate side-chains 150 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 0.0050 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.109004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.085293 restraints weight = 29930.052| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.47 r_work: 0.3529 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10716 Z= 0.148 Angle : 0.599 10.135 14505 Z= 0.312 Chirality : 0.044 0.178 1578 Planarity : 0.004 0.077 1859 Dihedral : 5.577 49.933 1437 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.03 % Allowed : 25.73 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.23), residues: 1295 helix: -0.57 (0.60), residues: 74 sheet: -0.22 (0.26), residues: 463 loop : -1.25 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 339 TYR 0.011 0.001 TYR C 53 PHE 0.038 0.001 PHE A 221 TRP 0.008 0.001 TRP C 52 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00335 (10683) covalent geometry : angle 0.59767 (14439) SS BOND : bond 0.00339 ( 33) SS BOND : angle 0.88894 ( 66) hydrogen bonds : bond 0.03122 ( 333) hydrogen bonds : angle 5.86234 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 112 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8480 (ptm160) cc_final: 0.8248 (ptp-170) REVERT: A 345 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7855 (mtpp) REVERT: A 435 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8454 (mmtt) REVERT: A 567 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8442 (ttm170) REVERT: A 654 ARG cc_start: 0.8116 (tpm170) cc_final: 0.7639 (tpm170) REVERT: B 131 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.6091 (ppp) REVERT: C 109 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7290 (ttt90) REVERT: C 185 ASP cc_start: 0.7765 (t0) cc_final: 0.7498 (t0) REVERT: C 193 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8083 (tt) REVERT: D 31 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8211 (mm110) REVERT: D 63 LYS cc_start: 0.6603 (tptp) cc_final: 0.6314 (tptp) REVERT: D 140 GLU cc_start: 0.7737 (pp20) cc_final: 0.7489 (pp20) REVERT: D 195 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8050 (t) outliers start: 60 outliers final: 39 residues processed: 161 average time/residue: 0.1071 time to fit residues: 24.0395 Evaluate side-chains 148 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.106953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.083180 restraints weight = 29694.809| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 4.38 r_work: 0.3489 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10716 Z= 0.200 Angle : 0.639 9.774 14505 Z= 0.335 Chirality : 0.045 0.196 1578 Planarity : 0.004 0.063 1859 Dihedral : 5.767 49.007 1436 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.95 % Allowed : 26.49 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.23), residues: 1295 helix: -0.61 (0.62), residues: 74 sheet: -0.28 (0.26), residues: 463 loop : -1.28 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 339 TYR 0.014 0.002 TYR C 49 PHE 0.019 0.002 PHE C 157 TRP 0.008 0.001 TRP C 52 HIS 0.003 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00450 (10683) covalent geometry : angle 0.63642 (14439) SS BOND : bond 0.00426 ( 33) SS BOND : angle 1.00614 ( 66) hydrogen bonds : bond 0.03405 ( 333) hydrogen bonds : angle 6.03318 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 104 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8045 (mttt) cc_final: 0.7735 (ttmt) REVERT: A 345 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8065 (mtpp) REVERT: A 435 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8450 (mmtt) REVERT: A 567 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8515 (ttm170) REVERT: A 654 ARG cc_start: 0.8152 (tpm170) cc_final: 0.7653 (tpm170) REVERT: B 131 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6271 (ppp) REVERT: C 72 ARG cc_start: 0.9267 (ttp80) cc_final: 0.8983 (ttp80) REVERT: C 109 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7306 (ttt90) REVERT: C 185 ASP cc_start: 0.7773 (t0) cc_final: 0.7388 (t0) REVERT: C 193 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8101 (tt) REVERT: D 31 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8227 (mm110) REVERT: D 46 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6704 (m-10) REVERT: D 63 LYS cc_start: 0.6744 (tptp) cc_final: 0.6458 (tptp) REVERT: D 140 GLU cc_start: 0.7761 (pp20) cc_final: 0.7509 (pp20) REVERT: D 195 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8014 (t) outliers start: 59 outliers final: 43 residues processed: 154 average time/residue: 0.1114 time to fit residues: 23.4740 Evaluate side-chains 149 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 112 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 98 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.109637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.085994 restraints weight = 29601.747| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.43 r_work: 0.3546 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10716 Z= 0.125 Angle : 0.609 10.395 14505 Z= 0.315 Chirality : 0.044 0.207 1578 Planarity : 0.003 0.056 1859 Dihedral : 5.522 49.722 1436 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.27 % Allowed : 27.24 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.23), residues: 1295 helix: -0.60 (0.61), residues: 74 sheet: -0.20 (0.26), residues: 463 loop : -1.22 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 339 TYR 0.012 0.001 TYR B 108 PHE 0.018 0.001 PHE C 157 TRP 0.009 0.001 TRP B 87 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00285 (10683) covalent geometry : angle 0.60833 (14439) SS BOND : bond 0.00339 ( 33) SS BOND : angle 0.77411 ( 66) hydrogen bonds : bond 0.02963 ( 333) hydrogen bonds : angle 5.73260 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8233 (ptp-170) REVERT: A 345 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8063 (mtpp) REVERT: A 435 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8400 (mmtt) REVERT: A 567 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8379 (ttm170) REVERT: A 654 ARG cc_start: 0.8191 (tpm170) cc_final: 0.7703 (tpm170) REVERT: B 43 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8774 (tmtt) REVERT: B 131 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6138 (ppp) REVERT: C 72 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8933 (ttp80) REVERT: C 100 ASP cc_start: 0.8374 (m-30) cc_final: 0.7361 (t0) REVERT: C 109 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7259 (ttt90) REVERT: C 169 ASP cc_start: 0.9153 (m-30) cc_final: 0.8923 (m-30) REVERT: C 185 ASP cc_start: 0.7696 (t0) cc_final: 0.7317 (t0) REVERT: C 193 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8143 (tt) REVERT: D 31 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8245 (mm110) REVERT: D 63 LYS cc_start: 0.6597 (tptp) cc_final: 0.6325 (tptp) REVERT: D 140 GLU cc_start: 0.7751 (pp20) cc_final: 0.7504 (pp20) outliers start: 51 outliers final: 37 residues processed: 155 average time/residue: 0.1047 time to fit residues: 22.5328 Evaluate side-chains 149 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 228 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.109248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.085638 restraints weight = 29523.436| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.42 r_work: 0.3537 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10716 Z= 0.136 Angle : 0.626 10.281 14505 Z= 0.322 Chirality : 0.044 0.194 1578 Planarity : 0.004 0.072 1859 Dihedral : 5.416 47.305 1434 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.44 % Allowed : 26.99 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.24), residues: 1295 helix: -0.60 (0.61), residues: 74 sheet: -0.16 (0.26), residues: 459 loop : -1.22 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.013 0.001 TYR A 635 PHE 0.020 0.001 PHE C 157 TRP 0.008 0.001 TRP C 52 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00311 (10683) covalent geometry : angle 0.62509 (14439) SS BOND : bond 0.00336 ( 33) SS BOND : angle 0.80732 ( 66) hydrogen bonds : bond 0.02999 ( 333) hydrogen bonds : angle 5.70852 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.6386 (ptp) cc_final: 0.6164 (pmm) REVERT: A 269 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8511 (mtmm) REVERT: A 287 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8241 (ptp-170) REVERT: A 345 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8174 (mtpp) REVERT: A 435 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8414 (mmtt) REVERT: A 654 ARG cc_start: 0.8198 (tpm170) cc_final: 0.7707 (tpm170) REVERT: B 43 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8766 (tmtt) REVERT: B 131 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6226 (ppp) REVERT: C 72 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8897 (ttp80) REVERT: C 100 ASP cc_start: 0.8425 (m-30) cc_final: 0.7510 (t0) REVERT: C 109 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7268 (ttt90) REVERT: C 169 ASP cc_start: 0.9160 (m-30) cc_final: 0.8930 (m-30) REVERT: C 185 ASP cc_start: 0.7697 (t0) cc_final: 0.7317 (t0) REVERT: C 193 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8115 (tt) REVERT: D 31 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8264 (mm110) REVERT: D 63 LYS cc_start: 0.6561 (tptp) cc_final: 0.6287 (tptp) REVERT: D 140 GLU cc_start: 0.7776 (pp20) cc_final: 0.7531 (pp20) REVERT: D 177 TYR cc_start: 0.7160 (p90) cc_final: 0.6492 (p90) outliers start: 53 outliers final: 43 residues processed: 155 average time/residue: 0.0957 time to fit residues: 20.6489 Evaluate side-chains 158 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 228 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN C 68 ASN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.109251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085616 restraints weight = 29286.435| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.40 r_work: 0.3536 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10716 Z= 0.144 Angle : 0.629 10.237 14505 Z= 0.323 Chirality : 0.044 0.191 1578 Planarity : 0.004 0.071 1859 Dihedral : 5.406 46.674 1434 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.19 % Allowed : 27.16 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.24), residues: 1295 helix: -0.60 (0.61), residues: 74 sheet: -0.19 (0.26), residues: 459 loop : -1.21 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.012 0.001 TYR A 635 PHE 0.021 0.001 PHE C 157 TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00329 (10683) covalent geometry : angle 0.62806 (14439) SS BOND : bond 0.00342 ( 33) SS BOND : angle 0.83322 ( 66) hydrogen bonds : bond 0.03027 ( 333) hydrogen bonds : angle 5.70581 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8651 (mtmm) REVERT: A 287 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8193 (ptp-170) REVERT: A 345 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8223 (mtpp) REVERT: A 435 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8418 (mmtt) REVERT: A 654 ARG cc_start: 0.8240 (tpm170) cc_final: 0.7751 (tpm170) REVERT: B 43 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8756 (tmtt) REVERT: B 131 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6276 (ppp) REVERT: B 339 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7943 (tpp80) REVERT: C 72 ARG cc_start: 0.9156 (ttp80) cc_final: 0.8876 (ttp80) REVERT: C 100 ASP cc_start: 0.8374 (m-30) cc_final: 0.7474 (t0) REVERT: C 109 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7275 (ttt90) REVERT: C 169 ASP cc_start: 0.9179 (m-30) cc_final: 0.8951 (m-30) REVERT: C 185 ASP cc_start: 0.7716 (t0) cc_final: 0.7349 (t0) REVERT: C 193 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8145 (tt) REVERT: D 31 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8265 (mm110) REVERT: D 63 LYS cc_start: 0.6581 (tptp) cc_final: 0.6330 (tptp) REVERT: D 140 GLU cc_start: 0.7777 (pp20) cc_final: 0.7517 (pp20) REVERT: D 177 TYR cc_start: 0.7149 (p90) cc_final: 0.6482 (p90) REVERT: D 195 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8020 (t) outliers start: 50 outliers final: 41 residues processed: 150 average time/residue: 0.1037 time to fit residues: 21.5809 Evaluate side-chains 155 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 228 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.109107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.085326 restraints weight = 29688.692| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 4.43 r_work: 0.3533 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10716 Z= 0.146 Angle : 0.630 10.197 14505 Z= 0.323 Chirality : 0.044 0.188 1578 Planarity : 0.004 0.069 1859 Dihedral : 5.400 45.475 1434 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.44 % Allowed : 27.07 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.24), residues: 1295 helix: -0.61 (0.61), residues: 74 sheet: -0.19 (0.26), residues: 459 loop : -1.19 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.013 0.001 TYR A 635 PHE 0.021 0.001 PHE C 157 TRP 0.008 0.001 TRP C 52 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00333 (10683) covalent geometry : angle 0.62911 (14439) SS BOND : bond 0.00356 ( 33) SS BOND : angle 0.80975 ( 66) hydrogen bonds : bond 0.03006 ( 333) hydrogen bonds : angle 5.69985 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.68 seconds wall clock time: 52 minutes 46.53 seconds (3166.53 seconds total)