Starting phenix.real_space_refine on Wed Feb 14 23:23:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cde_16570/02_2024/8cde_16570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cde_16570/02_2024/8cde_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cde_16570/02_2024/8cde_16570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cde_16570/02_2024/8cde_16570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cde_16570/02_2024/8cde_16570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cde_16570/02_2024/8cde_16570.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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 Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 5.81, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 3.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.26 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: 3.48 Time building geometry restraints manager: 4.04 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: 100.61 - 107.28: 283 107.28 - 113.94: 5755 113.94 - 120.61: 4058 120.61 - 127.28: 4258 127.28 - 133.94: 85 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 2.440 nonbonded pdb=" OE1 GLU C 101 " pdb=" OH TYR C 191 " model vdw 2.211 2.440 nonbonded pdb=" N GLU C 141 " pdb=" OE1 GLU C 141 " model vdw 2.230 2.520 nonbonded pdb=" O VAL A 295 " pdb=" NZ LYS A 309 " model vdw 2.231 2.520 nonbonded pdb=" O ALA A 586 " pdb=" OG1 THR A 600 " model vdw 2.250 2.440 ... (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 ========== 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: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 17.320 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.360 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.940 ------------------------------------------------------------------------------- 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 10683 Z= 0.188 Angle : 0.714 13.889 14439 Z= 0.367 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (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 TRP 0.014 0.001 TRP B 87 HIS 0.003 0.001 HIS D 232 PHE 0.013 0.001 PHE B 307 TYR 0.026 0.001 TYR A 286 ARG 0.016 0.001 ARG B 339 *********************** 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 fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.268 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: 0.8641 (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: 0.2618 time to fit residues: 61.5288 Evaluate side-chains 138 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 358 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 139 ASN B 191 ASN B 240 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN C 70 GLN C 217 GLN D 59 GLN D 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10683 Z= 0.276 Angle : 0.643 9.206 14439 Z= 0.340 Chirality : 0.044 0.184 1578 Planarity : 0.004 0.042 1859 Dihedral : 7.149 54.376 1469 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.62 % Allowed : 23.55 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1295 helix: -1.02 (0.55), residues: 81 sheet: -0.41 (0.25), residues: 447 loop : -1.51 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 208 HIS 0.003 0.001 HIS B 240 PHE 0.019 0.002 PHE A 221 TYR 0.017 0.002 TYR A 286 ARG 0.005 0.001 ARG B 339 *********************** 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 186 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 119 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7823 (ttp80) REVERT: A 435 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8456 (mmtt) REVERT: B 36 ARG cc_start: 0.7592 (ttt90) cc_final: 0.7307 (ttt90) REVERT: B 276 ASP cc_start: 0.8593 (m-30) cc_final: 0.8294 (p0) REVERT: B 281 GLN cc_start: 0.7694 (tt0) cc_final: 0.7293 (tt0) REVERT: C 187 LYS cc_start: 0.9457 (mmmm) cc_final: 0.9212 (mmmm) REVERT: C 193 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8133 (tt) REVERT: D 31 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8021 (mm110) REVERT: D 63 LYS cc_start: 0.6711 (tptp) cc_final: 0.6393 (tptp) REVERT: D 140 GLU cc_start: 0.7331 (pp20) cc_final: 0.7116 (pp20) outliers start: 67 outliers final: 41 residues processed: 169 average time/residue: 0.2449 time to fit residues: 58.3835 Evaluate side-chains 145 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 438 ASP 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 A residue 662 ASP 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 145 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 235 ASN 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 300 PHE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 ASN 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 140 ASP 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 Chi-restraints excluded: chain D residue 236 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 359 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS D 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10683 Z= 0.224 Angle : 0.596 10.021 14439 Z= 0.314 Chirality : 0.044 0.209 1578 Planarity : 0.003 0.045 1859 Dihedral : 6.553 59.730 1452 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.62 % Allowed : 23.47 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.23), residues: 1295 helix: -0.91 (0.55), residues: 81 sheet: -0.37 (0.25), residues: 453 loop : -1.46 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 87 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE C 157 TYR 0.013 0.001 TYR C 49 ARG 0.003 0.001 ARG B 339 *********************** 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 178 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 111 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8460 (mmtt) REVERT: A 564 GLU cc_start: 0.7892 (mp0) cc_final: 0.7430 (mp0) REVERT: A 618 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 276 ASP cc_start: 0.8622 (m-30) cc_final: 0.8317 (p0) REVERT: B 339 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7934 (ttm110) REVERT: C 50 TYR cc_start: 0.7954 (m-80) cc_final: 0.7738 (m-80) REVERT: C 160 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7854 (ttm-80) REVERT: C 187 LYS cc_start: 0.9457 (mmmm) cc_final: 0.9204 (mmmm) REVERT: C 193 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8032 (tt) REVERT: D 31 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8018 (mm110) REVERT: D 46 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6370 (m-10) REVERT: D 63 LYS cc_start: 0.6686 (tptp) cc_final: 0.6345 (tptp) REVERT: D 195 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8047 (t) REVERT: D 203 GLN cc_start: 0.7672 (mt0) cc_final: 0.7430 (mp10) outliers start: 67 outliers final: 43 residues processed: 162 average time/residue: 0.2433 time to fit residues: 55.9009 Evaluate side-chains 147 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 99 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 308 CYS 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 600 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 662 ASP 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 132 THR 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 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 182 THR 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 191 LEU 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 115 optimal weight: 1.9990 chunk 88 optimal weight: 0.0020 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10683 Z= 0.174 Angle : 0.568 10.366 14439 Z= 0.298 Chirality : 0.043 0.176 1578 Planarity : 0.003 0.045 1859 Dihedral : 5.942 54.748 1445 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.28 % Allowed : 25.06 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.23), residues: 1295 helix: -0.76 (0.55), residues: 80 sheet: -0.26 (0.26), residues: 450 loop : -1.37 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.003 0.001 HIS A 645 PHE 0.029 0.001 PHE A 221 TYR 0.010 0.001 TYR C 53 ARG 0.003 0.000 ARG B 339 *********************** 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 179 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 116 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4797 (OUTLIER) cc_final: 0.4135 (mt0) REVERT: A 435 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8446 (mmtt) REVERT: A 564 GLU cc_start: 0.7966 (mp0) cc_final: 0.7680 (mp0) REVERT: A 567 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8433 (ttm170) REVERT: B 131 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6091 (ppp) REVERT: B 276 ASP cc_start: 0.8604 (m-30) cc_final: 0.8311 (p0) REVERT: B 334 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8774 (mtpp) REVERT: C 109 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6739 (ttt90) REVERT: C 160 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7518 (ttm-80) REVERT: C 187 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9207 (mmmm) REVERT: C 193 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8127 (tt) REVERT: D 31 GLN cc_start: 0.8183 (mm110) cc_final: 0.7974 (mm110) REVERT: D 46 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6400 (m-10) REVERT: D 63 LYS cc_start: 0.6466 (tptp) cc_final: 0.6161 (tptp) REVERT: D 195 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8025 (t) REVERT: D 203 GLN cc_start: 0.7714 (mt0) cc_final: 0.7477 (mp10) outliers start: 63 outliers final: 43 residues processed: 163 average time/residue: 0.2417 time to fit residues: 54.7870 Evaluate side-chains 159 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 253 ASN 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 312 LEU 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 567 ARG Chi-restraints excluded: chain A residue 621 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 132 THR Chi-restraints excluded: chain B residue 133 CYS 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 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 334 LYS 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 214 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 191 LEU 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 103 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 0.0370 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10683 Z= 0.154 Angle : 0.557 10.590 14439 Z= 0.288 Chirality : 0.043 0.167 1578 Planarity : 0.003 0.046 1859 Dihedral : 5.705 59.063 1441 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.87 % Allowed : 25.15 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.23), residues: 1295 helix: -0.66 (0.56), residues: 80 sheet: -0.15 (0.26), residues: 449 loop : -1.29 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.003 0.001 HIS A 645 PHE 0.026 0.001 PHE A 221 TYR 0.009 0.001 TYR C 53 ARG 0.004 0.000 ARG C 72 *********************** 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 193 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 123 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4615 (OUTLIER) cc_final: 0.3921 (mt0) REVERT: A 435 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8423 (mmtt) REVERT: A 442 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7963 (mmmt) REVERT: A 564 GLU cc_start: 0.7936 (mp0) cc_final: 0.7664 (mp0) REVERT: A 567 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8371 (ttm170) REVERT: B 131 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.6005 (ppp) REVERT: B 276 ASP cc_start: 0.8589 (m-30) cc_final: 0.8308 (p0) REVERT: C 109 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6653 (ttt90) REVERT: C 161 GLU cc_start: 0.8095 (tp30) cc_final: 0.7782 (mp0) REVERT: C 187 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9203 (mmmm) REVERT: C 193 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8135 (tt) REVERT: D 46 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: D 63 LYS cc_start: 0.6402 (tptp) cc_final: 0.6149 (tptp) REVERT: D 195 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8069 (t) outliers start: 70 outliers final: 40 residues processed: 178 average time/residue: 0.2374 time to fit residues: 58.9707 Evaluate side-chains 157 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 110 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 312 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 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 132 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 219 TYR Chi-restraints excluded: chain B residue 235 ASN 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 309 ASN 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 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 46 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 191 LEU 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 41 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10683 Z= 0.237 Angle : 0.601 10.122 14439 Z= 0.312 Chirality : 0.044 0.177 1578 Planarity : 0.004 0.078 1859 Dihedral : 5.696 59.365 1436 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.78 % Allowed : 25.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.23), residues: 1295 helix: -0.41 (0.61), residues: 74 sheet: -0.18 (0.26), residues: 459 loop : -1.31 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 208 HIS 0.004 0.001 HIS A 645 PHE 0.038 0.002 PHE A 221 TYR 0.012 0.001 TYR A 151 ARG 0.006 0.001 ARG C 160 *********************** 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 180 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 111 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4824 (OUTLIER) cc_final: 0.4163 (mt0) REVERT: A 435 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8489 (mmtt) REVERT: B 131 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.6205 (ppp) REVERT: B 334 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8775 (mtpp) REVERT: C 109 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6828 (ttt90) REVERT: C 187 LYS cc_start: 0.9454 (mmmm) cc_final: 0.9199 (mmmm) REVERT: C 193 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8150 (tt) REVERT: D 46 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6405 (m-10) REVERT: D 63 LYS cc_start: 0.6650 (tptp) cc_final: 0.6359 (tptp) REVERT: D 195 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8076 (t) outliers start: 69 outliers final: 52 residues processed: 164 average time/residue: 0.2467 time to fit residues: 55.9982 Evaluate side-chains 166 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 107 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain A residue 95 ASP 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 205 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 253 ASN 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 369 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 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 132 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 334 LYS 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 182 THR 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 139 THR 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 191 LEU 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 14 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10683 Z= 0.202 Angle : 0.598 10.336 14439 Z= 0.308 Chirality : 0.044 0.204 1578 Planarity : 0.004 0.070 1859 Dihedral : 5.650 56.576 1436 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.04 % Allowed : 26.07 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.23), residues: 1295 helix: -0.37 (0.61), residues: 74 sheet: -0.15 (0.26), residues: 447 loop : -1.32 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 208 HIS 0.004 0.001 HIS A 645 PHE 0.032 0.001 PHE A 221 TYR 0.010 0.001 TYR A 635 ARG 0.006 0.001 ARG B 174 *********************** 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 182 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 110 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4713 (OUTLIER) cc_final: 0.4035 (mt0) REVERT: A 287 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (ptp-170) REVERT: A 435 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8420 (mmtt) REVERT: A 436 MET cc_start: 0.8570 (pmm) cc_final: 0.8339 (pmm) REVERT: A 442 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7936 (mmmt) REVERT: A 564 GLU cc_start: 0.7985 (mp0) cc_final: 0.7680 (mp0) REVERT: B 131 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6271 (ppp) REVERT: B 334 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8775 (mtpp) REVERT: C 109 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.6792 (ttt90) REVERT: C 193 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8103 (tt) REVERT: D 46 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6389 (m-10) REVERT: D 63 LYS cc_start: 0.6640 (tptp) cc_final: 0.6430 (tptp) REVERT: D 195 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8048 (t) outliers start: 72 outliers final: 53 residues processed: 167 average time/residue: 0.2468 time to fit residues: 57.5763 Evaluate side-chains 166 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 105 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 253 ASN 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 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 631 LEU 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 97 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 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 182 THR 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 139 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 191 LEU 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 49 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10683 Z= 0.228 Angle : 0.611 10.178 14439 Z= 0.314 Chirality : 0.044 0.187 1578 Planarity : 0.004 0.071 1859 Dihedral : 5.654 54.427 1436 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.29 % Allowed : 25.82 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1295 helix: -0.36 (0.62), residues: 74 sheet: -0.20 (0.26), residues: 447 loop : -1.30 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 208 HIS 0.003 0.001 HIS A 645 PHE 0.020 0.001 PHE C 157 TYR 0.011 0.001 TYR A 635 ARG 0.004 0.001 ARG B 174 *********************** 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 181 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 106 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4767 (OUTLIER) cc_final: 0.4075 (mt0) REVERT: A 435 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8447 (mmtt) REVERT: A 436 MET cc_start: 0.8575 (pmm) cc_final: 0.8341 (pmm) REVERT: A 564 GLU cc_start: 0.8032 (mp0) cc_final: 0.7604 (mp0) REVERT: A 585 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7795 (tptm) REVERT: B 131 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.6484 (ppp) REVERT: B 334 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8762 (mtpp) REVERT: C 100 ASP cc_start: 0.8492 (m-30) cc_final: 0.7362 (t0) REVERT: C 109 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.6831 (ttt90) REVERT: C 193 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8129 (tt) REVERT: D 46 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6400 (m-10) REVERT: D 63 LYS cc_start: 0.6665 (tptp) cc_final: 0.6449 (tptp) REVERT: D 177 TYR cc_start: 0.7388 (p90) cc_final: 0.6588 (p90) REVERT: D 195 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8058 (t) outliers start: 75 outliers final: 60 residues processed: 167 average time/residue: 0.2455 time to fit residues: 56.8895 Evaluate side-chains 173 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 105 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 253 ASN 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 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 631 LEU 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 97 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 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 182 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 LEU 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 191 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10683 Z= 0.210 Angle : 0.603 10.270 14439 Z= 0.311 Chirality : 0.044 0.186 1578 Planarity : 0.004 0.071 1859 Dihedral : 5.592 52.038 1436 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.20 % Allowed : 25.73 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1295 helix: -0.35 (0.62), residues: 74 sheet: -0.18 (0.27), residues: 447 loop : -1.26 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.003 0.001 HIS A 645 PHE 0.021 0.001 PHE C 157 TYR 0.010 0.001 TYR A 635 ARG 0.004 0.001 ARG B 174 *********************** 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 182 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 108 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4588 (OUTLIER) cc_final: 0.3912 (mt0) REVERT: A 287 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8221 (ptp-170) REVERT: A 435 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8453 (mmtt) REVERT: A 436 MET cc_start: 0.8555 (pmm) cc_final: 0.8329 (pmm) REVERT: A 564 GLU cc_start: 0.8036 (mp0) cc_final: 0.7586 (mp0) REVERT: A 585 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7770 (tptm) REVERT: B 108 TYR cc_start: 0.7946 (m-80) cc_final: 0.7594 (m-80) REVERT: B 131 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6380 (ppp) REVERT: B 334 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8765 (mtpp) REVERT: C 100 ASP cc_start: 0.8473 (m-30) cc_final: 0.7356 (t0) REVERT: C 109 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.6801 (ttt90) REVERT: C 193 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8154 (tt) REVERT: D 46 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6440 (m-10) REVERT: D 63 LYS cc_start: 0.6643 (tptp) cc_final: 0.6385 (tptp) REVERT: D 177 TYR cc_start: 0.7456 (p90) cc_final: 0.6662 (p90) REVERT: D 195 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8049 (t) outliers start: 74 outliers final: 59 residues processed: 169 average time/residue: 0.2405 time to fit residues: 56.3912 Evaluate side-chains 175 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 107 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 253 ASN 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 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 338 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 182 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 LEU 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 191 LEU 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 74 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10683 Z= 0.181 Angle : 0.605 10.475 14439 Z= 0.308 Chirality : 0.044 0.183 1578 Planarity : 0.003 0.070 1859 Dihedral : 5.507 51.296 1436 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.53 % Allowed : 26.74 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1295 helix: -0.38 (0.61), residues: 74 sheet: -0.16 (0.27), residues: 449 loop : -1.24 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.003 0.001 HIS D 232 PHE 0.021 0.001 PHE C 157 TYR 0.009 0.001 TYR A 635 ARG 0.005 0.000 ARG B 339 ********************** 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 174 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 108 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.4500 (OUTLIER) cc_final: 0.3774 (mt0) REVERT: A 287 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8183 (ttm170) REVERT: A 435 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8432 (mmtt) REVERT: A 436 MET cc_start: 0.8535 (pmm) cc_final: 0.8287 (pmm) REVERT: A 564 GLU cc_start: 0.8016 (mp0) cc_final: 0.7544 (mp0) REVERT: A 585 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7799 (tptm) REVERT: B 131 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6270 (ppp) REVERT: C 109 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6778 (ttt90) REVERT: C 193 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8145 (tt) REVERT: D 46 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6342 (m-10) REVERT: D 63 LYS cc_start: 0.6634 (tptp) cc_final: 0.6375 (tptp) REVERT: D 177 TYR cc_start: 0.7447 (p90) cc_final: 0.6666 (p90) REVERT: D 195 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8011 (t) outliers start: 66 outliers final: 51 residues processed: 163 average time/residue: 0.2646 time to fit residues: 60.7964 Evaluate side-chains 165 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 106 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ASP 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 369 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 585 LYS 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 82 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 235 ASN 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 309 ASN Chi-restraints excluded: chain B residue 338 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 160 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 219 LEU 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 191 LEU Chi-restraints excluded: chain D residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** 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 = 0.4113 r_free = 0.4113 target = 0.107478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083850 restraints weight = 29579.400| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 4.35 r_work: 0.3504 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10683 Z= 0.252 Angle : 0.633 10.061 14439 Z= 0.325 Chirality : 0.045 0.178 1578 Planarity : 0.004 0.071 1859 Dihedral : 5.586 49.380 1433 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.53 % Allowed : 26.49 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1295 helix: -0.37 (0.62), residues: 74 sheet: -0.25 (0.27), residues: 450 loop : -1.32 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 208 HIS 0.003 0.001 HIS A 645 PHE 0.022 0.001 PHE C 157 TYR 0.012 0.001 TYR A 635 ARG 0.004 0.001 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.21 seconds wall clock time: 52 minutes 52.59 seconds (3172.59 seconds total)