Starting phenix.real_space_refine on Tue Jul 29 04:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qfc_18381/07_2025/8qfc_18381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qfc_18381/07_2025/8qfc_18381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qfc_18381/07_2025/8qfc_18381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qfc_18381/07_2025/8qfc_18381.map" model { file = "/net/cci-nas-00/data/ceres_data/8qfc_18381/07_2025/8qfc_18381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qfc_18381/07_2025/8qfc_18381.cif" } resolution = 3.2 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= 0.000 sd= 0.012 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 35 5.16 5 C 6975 2.51 5 N 1892 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10968 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1680 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4710 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 14, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 23, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 178 Chain: "C" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2853 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 10, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU:plan': 15, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "D" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1156 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 1, 'TRANS': 183} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 34, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 276 Chain: "E" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 569 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 10.07, per 1000 atoms: 0.92 Number of scatterers: 10968 At special positions: 0 Unit cell: (230.14, 187.96, 101.38, 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 35 16.00 O 2066 8.00 N 1892 7.00 C 6975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 69.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.568A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.651A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 removed outlier: 3.666A pdb=" N TYR A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.663A pdb=" N LYS A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 118' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 152 Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 58 through 73 removed outlier: 4.011A pdb=" N SER B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 89 through 104 removed outlier: 3.883A pdb=" N ILE B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 135 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 149 through 160 removed outlier: 3.620A pdb=" N ARG B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.653A pdb=" N VAL B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 279 through 288 removed outlier: 3.729A pdb=" N LYS B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 320 Processing helix chain 'B' and resid 326 through 329 Processing helix chain 'B' and resid 334 through 347 Processing helix chain 'B' and resid 365 through 388 removed outlier: 3.649A pdb=" N GLU B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 494 through 524 removed outlier: 4.497A pdb=" N LYS B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 536 through 561 removed outlier: 3.922A pdb=" N GLU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 552 " --> pdb=" O TYR B 548 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 554 " --> pdb=" O ASN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 594 removed outlier: 4.209A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 585 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.692A pdb=" N ILE B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 613 Processing helix chain 'B' and resid 616 through 629 removed outlier: 3.849A pdb=" N ALA B 622 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 635 through 649 Processing helix chain 'B' and resid 657 through 679 Processing helix chain 'B' and resid 681 through 699 Processing helix chain 'B' and resid 708 through 717 removed outlier: 3.756A pdb=" N ILE B 712 " --> pdb=" O CYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.885A pdb=" N HIS B 725 " --> pdb=" O PRO B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 786 removed outlier: 3.553A pdb=" N ILE B 779 " --> pdb=" O LEU B 775 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 780 " --> pdb=" O SER B 776 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.847A pdb=" N LEU C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 79 removed outlier: 4.093A pdb=" N GLY C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 106 removed outlier: 4.279A pdb=" N LYS C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TRP C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 125 removed outlier: 3.646A pdb=" N GLU C 125 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 168 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 188 through 199 removed outlier: 3.802A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.997A pdb=" N LYS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 346 through 373 removed outlier: 4.326A pdb=" N GLU C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 394 through 418 removed outlier: 3.628A pdb=" N MET C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 425 removed outlier: 3.556A pdb=" N LEU C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 469 Processing helix chain 'C' and resid 469 through 494 removed outlier: 4.432A pdb=" N ASP C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 188 removed outlier: 3.615A pdb=" N GLU D 138 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 241 through 256 Processing helix chain 'D' and resid 272 through 287 removed outlier: 3.540A pdb=" N GLY D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 302 Processing helix chain 'E' and resid 28 through 41 removed outlier: 4.273A pdb=" N VAL E 32 " --> pdb=" O PRO E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.756A pdb=" N VAL E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 171 removed outlier: 6.432A pdb=" N CYS A 164 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU A 38 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA A 166 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 36 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA A 168 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 34 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 33 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A 206 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A 35 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 204 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER A 37 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 204 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.521A pdb=" N SER A 113 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AA8, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AA9, first strand: chain 'B' and resid 322 through 324 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.360A pdb=" N ILE C 9 " --> pdb=" O ASN C 500 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET C 502 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 11 " --> pdb=" O MET C 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 197 through 203 removed outlier: 5.518A pdb=" N VAL D 198 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N SER E 22 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E 21 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E 6 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU E 74 " --> pdb=" O SER E 5 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS E 7 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE E 76 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR E 9 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 228 through 229 removed outlier: 3.684A pdb=" N LYS D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2286 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: 3.66 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3671 1.34 - 1.46: 2254 1.46 - 1.58: 5146 1.58 - 1.70: 1 1.70 - 1.81: 53 Bond restraints: 11125 Sorted by residual: bond pdb=" CB PRO C 498 " pdb=" CG PRO C 498 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 9.01e+00 bond pdb=" N SER E 2 " pdb=" CA SER E 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLN C 5 " pdb=" CA GLN C 5 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N SER A 2 " pdb=" CA SER A 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N LEU B 27 " pdb=" CA LEU B 27 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.34e+00 ... (remaining 11120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 14986 2.32 - 4.64: 141 4.64 - 6.96: 6 6.96 - 9.28: 3 9.28 - 11.60: 1 Bond angle restraints: 15137 Sorted by residual: angle pdb=" CA PRO C 498 " pdb=" N PRO C 498 " pdb=" CD PRO C 498 " ideal model delta sigma weight residual 112.00 100.40 11.60 1.40e+00 5.10e-01 6.86e+01 angle pdb=" CA GLN C 458 " pdb=" CB GLN C 458 " pdb=" CG GLN C 458 " ideal model delta sigma weight residual 114.10 121.24 -7.14 2.00e+00 2.50e-01 1.28e+01 angle pdb=" N PRO C 498 " pdb=" CD PRO C 498 " pdb=" CG PRO C 498 " ideal model delta sigma weight residual 103.20 97.99 5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C THR A 175 " pdb=" N ASP A 176 " pdb=" CA ASP A 176 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.68e+00 angle pdb=" CB GLN C 458 " pdb=" CG GLN C 458 " pdb=" CD GLN C 458 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.70e+00 3.46e-01 6.62e+00 ... (remaining 15132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5908 17.67 - 35.35: 617 35.35 - 53.02: 182 53.02 - 70.69: 21 70.69 - 88.37: 15 Dihedral angle restraints: 6743 sinusoidal: 2374 harmonic: 4369 Sorted by residual: dihedral pdb=" CA GLY D 204 " pdb=" C GLY D 204 " pdb=" N GLU D 205 " pdb=" CA GLU D 205 " ideal model delta harmonic sigma weight residual -180.00 -160.41 -19.59 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE B 554 " pdb=" C PHE B 554 " pdb=" N GLU B 555 " pdb=" CA GLU B 555 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA VAL D 197 " pdb=" C VAL D 197 " pdb=" N VAL D 198 " pdb=" CA VAL D 198 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1342 0.034 - 0.068: 372 0.068 - 0.102: 107 0.102 - 0.137: 50 0.137 - 0.171: 1 Chirality restraints: 1872 Sorted by residual: chirality pdb=" CA PRO C 498 " pdb=" N PRO C 498 " pdb=" C PRO C 498 " pdb=" CB PRO C 498 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE E 57 " pdb=" N ILE E 57 " pdb=" C ILE E 57 " pdb=" CB ILE E 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL C 7 " pdb=" N VAL C 7 " pdb=" C VAL C 7 " pdb=" CB VAL C 7 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1869 not shown) Planarity restraints: 1935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 497 " -0.079 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO C 498 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO C 498 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 498 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 176 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ASP A 176 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A 176 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 177 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 599 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 600 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 600 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 600 " 0.030 5.00e-02 4.00e+02 ... (remaining 1932 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 93 2.53 - 3.12: 9168 3.12 - 3.72: 17527 3.72 - 4.31: 22448 4.31 - 4.90: 37525 Nonbonded interactions: 86761 Sorted by model distance: nonbonded pdb=" O PHE B 521 " pdb=" OG1 THR B 525 " model vdw 1.940 3.040 nonbonded pdb=" O LYS B 625 " pdb=" OG SER B 629 " model vdw 1.954 3.040 nonbonded pdb=" OD1 ASP C 376 " pdb=" OG SER C 379 " model vdw 2.003 3.040 nonbonded pdb=" O LYS B 610 " pdb=" OG SER B 613 " model vdw 2.032 3.040 nonbonded pdb=" O THR D 242 " pdb=" OG1 THR D 245 " model vdw 2.068 3.040 ... (remaining 86756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.87 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: 11.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 11125 Z= 0.174 Angle : 0.566 11.598 15137 Z= 0.317 Chirality : 0.038 0.171 1872 Planarity : 0.005 0.110 1935 Dihedral : 16.429 88.366 3883 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.09 % Allowed : 26.71 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.22), residues: 1466 helix: 1.47 (0.17), residues: 962 sheet: -1.27 (0.60), residues: 75 loop : -1.52 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 198 HIS 0.010 0.001 HIS B 572 PHE 0.014 0.001 PHE B 476 TYR 0.014 0.001 TYR B 146 ARG 0.005 0.000 ARG B 660 Details of bonding type rmsd hydrogen bonds : bond 0.15169 ( 776) hydrogen bonds : angle 6.07494 ( 2286) covalent geometry : bond 0.00391 (11125) covalent geometry : angle 0.56636 (15137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8153 (m-30) cc_final: 0.7748 (m-30) REVERT: A 92 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8398 (ttmm) REVERT: B 132 GLN cc_start: 0.8380 (mt0) cc_final: 0.8088 (mt0) REVERT: B 158 THR cc_start: 0.8601 (m) cc_final: 0.8281 (p) REVERT: B 318 SER cc_start: 0.8723 (m) cc_final: 0.8449 (p) REVERT: B 370 ASN cc_start: 0.8613 (m-40) cc_final: 0.8404 (m110) REVERT: C 385 LEU cc_start: 0.8490 (mp) cc_final: 0.8150 (mm) REVERT: C 445 GLN cc_start: 0.7573 (mt0) cc_final: 0.7291 (mp10) REVERT: D 247 ASN cc_start: 0.7817 (m-40) cc_final: 0.7453 (m110) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.2920 time to fit residues: 121.6697 Evaluate side-chains 307 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 140 HIS A 158 GLN B 95 ASN B 132 GLN B 151 ASN C 209 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.145216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129178 restraints weight = 25231.935| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.93 r_work: 0.3718 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11125 Z= 0.161 Angle : 0.598 10.281 15137 Z= 0.312 Chirality : 0.042 0.218 1872 Planarity : 0.004 0.073 1935 Dihedral : 4.243 23.818 1565 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.37 % Allowed : 24.43 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.22), residues: 1466 helix: 1.74 (0.16), residues: 983 sheet: -0.19 (0.66), residues: 66 loop : -1.48 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 241 HIS 0.006 0.001 HIS B 572 PHE 0.032 0.002 PHE B 696 TYR 0.017 0.001 TYR C 104 ARG 0.004 0.001 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 776) hydrogen bonds : angle 4.92906 ( 2286) covalent geometry : bond 0.00345 (11125) covalent geometry : angle 0.59807 (15137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8408 (m-30) cc_final: 0.7888 (m-30) REVERT: A 72 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: A 92 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8457 (ttmm) REVERT: B 81 ASP cc_start: 0.7697 (t0) cc_final: 0.7424 (t0) REVERT: B 318 SER cc_start: 0.8550 (m) cc_final: 0.8198 (p) REVERT: B 370 ASN cc_start: 0.8837 (m-40) cc_final: 0.8548 (m110) REVERT: C 226 MET cc_start: 0.7886 (ttm) cc_final: 0.7652 (ttp) REVERT: C 379 SER cc_start: 0.8639 (m) cc_final: 0.8292 (m) REVERT: C 385 LEU cc_start: 0.8532 (mp) cc_final: 0.8212 (mm) REVERT: C 445 GLN cc_start: 0.7911 (mt0) cc_final: 0.7474 (mp10) REVERT: D 247 ASN cc_start: 0.8071 (m-40) cc_final: 0.7779 (m110) outliers start: 37 outliers final: 16 residues processed: 321 average time/residue: 0.2623 time to fit residues: 113.6380 Evaluate side-chains 302 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 81 optimal weight: 0.0010 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 95 ASN B 132 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.144317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.128390 restraints weight = 25835.102| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.98 r_work: 0.3708 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11125 Z= 0.171 Angle : 0.586 10.392 15137 Z= 0.305 Chirality : 0.041 0.179 1872 Planarity : 0.004 0.052 1935 Dihedral : 4.224 20.656 1565 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.74 % Allowed : 24.25 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.22), residues: 1466 helix: 1.79 (0.16), residues: 984 sheet: -0.01 (0.67), residues: 66 loop : -1.36 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.009 0.001 HIS C 419 PHE 0.042 0.002 PHE B 696 TYR 0.018 0.001 TYR C 104 ARG 0.003 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 776) hydrogen bonds : angle 4.72480 ( 2286) covalent geometry : bond 0.00380 (11125) covalent geometry : angle 0.58562 (15137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: A 92 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8438 (ttmm) REVERT: B 67 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7759 (mmt90) REVERT: B 293 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8461 (mt) REVERT: B 318 SER cc_start: 0.8485 (m) cc_final: 0.8126 (p) REVERT: B 370 ASN cc_start: 0.8842 (m-40) cc_final: 0.8534 (m110) REVERT: C 226 MET cc_start: 0.7962 (ttm) cc_final: 0.7706 (ttp) REVERT: C 385 LEU cc_start: 0.8536 (mp) cc_final: 0.8228 (mm) REVERT: D 247 ASN cc_start: 0.8106 (m-40) cc_final: 0.7852 (m-40) outliers start: 52 outliers final: 29 residues processed: 316 average time/residue: 0.2981 time to fit residues: 127.7697 Evaluate side-chains 313 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain E residue 6 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 106 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 0.2980 chunk 132 optimal weight: 0.0570 chunk 97 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 95 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.144837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.128915 restraints weight = 25621.189| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.02 r_work: 0.3718 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11125 Z= 0.143 Angle : 0.567 8.989 15137 Z= 0.296 Chirality : 0.040 0.162 1872 Planarity : 0.004 0.051 1935 Dihedral : 4.120 19.083 1565 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.56 % Allowed : 25.43 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.22), residues: 1466 helix: 1.91 (0.17), residues: 983 sheet: 0.12 (0.68), residues: 66 loop : -1.30 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 19 HIS 0.007 0.001 HIS C 419 PHE 0.031 0.001 PHE B 696 TYR 0.021 0.001 TYR C 104 ARG 0.007 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 776) hydrogen bonds : angle 4.55658 ( 2286) covalent geometry : bond 0.00313 (11125) covalent geometry : angle 0.56697 (15137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: A 92 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8422 (ttmm) REVERT: A 114 GLU cc_start: 0.8071 (pm20) cc_final: 0.7844 (mp0) REVERT: B 67 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7786 (mmt90) REVERT: B 293 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 318 SER cc_start: 0.8469 (m) cc_final: 0.8124 (p) REVERT: B 370 ASN cc_start: 0.8828 (m-40) cc_final: 0.8518 (m110) REVERT: B 479 GLN cc_start: 0.8174 (pm20) cc_final: 0.7925 (pm20) REVERT: C 10 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6649 (m-30) REVERT: C 226 MET cc_start: 0.7945 (ttm) cc_final: 0.7680 (ttp) REVERT: C 385 LEU cc_start: 0.8535 (mp) cc_final: 0.8234 (mm) REVERT: C 445 GLN cc_start: 0.7854 (mt0) cc_final: 0.7301 (mp10) REVERT: D 237 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8259 (mm110) outliers start: 50 outliers final: 31 residues processed: 316 average time/residue: 0.2523 time to fit residues: 108.3810 Evaluate side-chains 321 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 63 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 95 ASN B 113 GLN B 132 GLN B 308 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.143749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127903 restraints weight = 25520.500| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.97 r_work: 0.3700 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11125 Z= 0.182 Angle : 0.616 11.768 15137 Z= 0.318 Chirality : 0.041 0.230 1872 Planarity : 0.004 0.052 1935 Dihedral : 4.205 19.937 1565 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.10 % Allowed : 26.07 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.22), residues: 1466 helix: 1.86 (0.17), residues: 984 sheet: 0.14 (0.68), residues: 66 loop : -1.33 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 19 HIS 0.011 0.002 HIS C 419 PHE 0.028 0.002 PHE B 696 TYR 0.020 0.001 TYR E 18 ARG 0.005 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 776) hydrogen bonds : angle 4.64289 ( 2286) covalent geometry : bond 0.00405 (11125) covalent geometry : angle 0.61617 (15137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: A 92 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8403 (ttmm) REVERT: A 114 GLU cc_start: 0.8040 (pm20) cc_final: 0.7778 (mp0) REVERT: B 67 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7796 (mmt90) REVERT: B 251 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (ttm-80) REVERT: B 293 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8485 (mt) REVERT: B 318 SER cc_start: 0.8502 (m) cc_final: 0.8164 (p) REVERT: B 370 ASN cc_start: 0.8835 (m-40) cc_final: 0.8523 (m110) REVERT: C 385 LEU cc_start: 0.8556 (mp) cc_final: 0.8243 (mm) REVERT: C 445 GLN cc_start: 0.7926 (mt0) cc_final: 0.7413 (mp10) REVERT: D 237 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8274 (mm110) outliers start: 56 outliers final: 36 residues processed: 321 average time/residue: 0.2760 time to fit residues: 120.6457 Evaluate side-chains 327 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 171 HIS B 95 ASN B 132 GLN B 308 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.143608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.127703 restraints weight = 25428.251| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.95 r_work: 0.3694 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11125 Z= 0.196 Angle : 0.621 10.633 15137 Z= 0.323 Chirality : 0.042 0.311 1872 Planarity : 0.004 0.053 1935 Dihedral : 4.282 21.133 1565 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.29 % Allowed : 26.98 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1466 helix: 1.79 (0.17), residues: 984 sheet: 0.00 (0.68), residues: 66 loop : -1.37 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 241 HIS 0.010 0.002 HIS C 419 PHE 0.026 0.002 PHE B 696 TYR 0.020 0.001 TYR C 104 ARG 0.004 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 776) hydrogen bonds : angle 4.67948 ( 2286) covalent geometry : bond 0.00438 (11125) covalent geometry : angle 0.62129 (15137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 295 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: A 92 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8423 (ttmm) REVERT: A 114 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 67 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7803 (mmt90) REVERT: B 129 ASP cc_start: 0.7843 (m-30) cc_final: 0.7623 (m-30) REVERT: B 251 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: B 293 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 318 SER cc_start: 0.8498 (m) cc_final: 0.8167 (p) REVERT: B 370 ASN cc_start: 0.8836 (m-40) cc_final: 0.8534 (m110) REVERT: C 218 SER cc_start: 0.8668 (t) cc_final: 0.8369 (p) REVERT: C 226 MET cc_start: 0.7860 (ttp) cc_final: 0.7608 (ttp) REVERT: C 227 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (mp) REVERT: C 385 LEU cc_start: 0.8572 (mp) cc_final: 0.8248 (mm) REVERT: C 445 GLN cc_start: 0.7946 (mt0) cc_final: 0.7463 (mp10) REVERT: D 237 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8299 (mm110) outliers start: 58 outliers final: 42 residues processed: 326 average time/residue: 0.2721 time to fit residues: 120.4096 Evaluate side-chains 338 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 13 optimal weight: 0.0670 chunk 71 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 142 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 95 ASN B 132 GLN C 393 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.144673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.128726 restraints weight = 25942.884| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.03 r_work: 0.3716 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11125 Z= 0.137 Angle : 0.619 12.921 15137 Z= 0.315 Chirality : 0.041 0.336 1872 Planarity : 0.004 0.052 1935 Dihedral : 4.137 20.317 1565 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.01 % Allowed : 27.89 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.22), residues: 1466 helix: 1.94 (0.17), residues: 982 sheet: 0.09 (0.68), residues: 66 loop : -1.29 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 PHE 0.023 0.001 PHE B 696 TYR 0.017 0.001 TYR C 104 ARG 0.004 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 776) hydrogen bonds : angle 4.54139 ( 2286) covalent geometry : bond 0.00302 (11125) covalent geometry : angle 0.61905 (15137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: A 92 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8406 (ttmm) REVERT: A 114 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: B 67 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7781 (mmt90) REVERT: B 68 ASP cc_start: 0.8187 (m-30) cc_final: 0.7975 (m-30) REVERT: B 129 ASP cc_start: 0.7851 (m-30) cc_final: 0.7630 (m-30) REVERT: B 251 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7898 (ttm-80) REVERT: B 293 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 318 SER cc_start: 0.8467 (m) cc_final: 0.8135 (p) REVERT: B 370 ASN cc_start: 0.8814 (m-40) cc_final: 0.8489 (m110) REVERT: C 10 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: C 218 SER cc_start: 0.8665 (t) cc_final: 0.8372 (p) REVERT: C 226 MET cc_start: 0.7805 (ttp) cc_final: 0.7590 (ttp) REVERT: C 227 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8006 (mp) REVERT: C 385 LEU cc_start: 0.8565 (mp) cc_final: 0.8246 (mm) REVERT: C 407 ASP cc_start: 0.8089 (t0) cc_final: 0.7845 (t0) REVERT: C 445 GLN cc_start: 0.7936 (mt0) cc_final: 0.7471 (mp10) REVERT: C 486 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8095 (mt) REVERT: D 237 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8274 (mm110) outliers start: 55 outliers final: 35 residues processed: 318 average time/residue: 0.2668 time to fit residues: 114.3309 Evaluate side-chains 325 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 6 PHE Chi-restraints excluded: chain E residue 25 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 89 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 144 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 95 ASN B 132 GLN C 393 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.144986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129039 restraints weight = 25462.299| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.96 r_work: 0.3717 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11125 Z= 0.146 Angle : 0.627 12.811 15137 Z= 0.320 Chirality : 0.042 0.345 1872 Planarity : 0.004 0.053 1935 Dihedral : 4.083 19.926 1565 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.10 % Allowed : 29.26 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.22), residues: 1466 helix: 1.94 (0.17), residues: 987 sheet: 0.08 (0.68), residues: 66 loop : -1.24 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 PHE 0.022 0.001 PHE B 696 TYR 0.032 0.001 TYR C 104 ARG 0.003 0.000 ARG D 286 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 776) hydrogen bonds : angle 4.51297 ( 2286) covalent geometry : bond 0.00325 (11125) covalent geometry : angle 0.62694 (15137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 92 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8384 (ttmm) REVERT: A 114 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: B 67 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7769 (mmt90) REVERT: B 68 ASP cc_start: 0.8184 (m-30) cc_final: 0.7973 (m-30) REVERT: B 129 ASP cc_start: 0.7849 (m-30) cc_final: 0.7644 (m-30) REVERT: B 251 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7908 (ttm-80) REVERT: B 293 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (mt) REVERT: B 318 SER cc_start: 0.8452 (m) cc_final: 0.8117 (p) REVERT: B 370 ASN cc_start: 0.8807 (m-40) cc_final: 0.8482 (m110) REVERT: B 481 GLU cc_start: 0.7995 (mp0) cc_final: 0.7649 (mp0) REVERT: C 10 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: C 218 SER cc_start: 0.8664 (t) cc_final: 0.8375 (p) REVERT: C 226 MET cc_start: 0.7845 (ttp) cc_final: 0.7591 (ttp) REVERT: C 227 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 358 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8156 (mtp) REVERT: C 385 LEU cc_start: 0.8573 (mp) cc_final: 0.8262 (mm) REVERT: C 407 ASP cc_start: 0.8089 (t0) cc_final: 0.7847 (t0) REVERT: C 445 GLN cc_start: 0.7937 (mt0) cc_final: 0.7479 (mp10) REVERT: C 486 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8107 (mt) outliers start: 45 outliers final: 31 residues processed: 317 average time/residue: 0.2785 time to fit residues: 121.2097 Evaluate side-chains 320 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 6 PHE Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 134 optimal weight: 0.0050 chunk 146 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 393 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.144479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128585 restraints weight = 25925.354| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.02 r_work: 0.3712 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11125 Z= 0.158 Angle : 0.650 12.966 15137 Z= 0.334 Chirality : 0.043 0.347 1872 Planarity : 0.004 0.056 1935 Dihedral : 4.121 20.223 1565 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.10 % Allowed : 29.35 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.22), residues: 1466 helix: 1.92 (0.17), residues: 988 sheet: 0.09 (0.68), residues: 66 loop : -1.27 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 PHE 0.019 0.001 PHE B 696 TYR 0.027 0.001 TYR C 104 ARG 0.013 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 776) hydrogen bonds : angle 4.58274 ( 2286) covalent geometry : bond 0.00354 (11125) covalent geometry : angle 0.64994 (15137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: A 92 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8371 (ttmm) REVERT: A 114 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 67 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7802 (mmt90) REVERT: B 68 ASP cc_start: 0.8198 (m-30) cc_final: 0.7986 (m-30) REVERT: B 251 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7917 (ttm-80) REVERT: B 293 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 318 SER cc_start: 0.8459 (m) cc_final: 0.8123 (p) REVERT: B 370 ASN cc_start: 0.8814 (m-40) cc_final: 0.8506 (m110) REVERT: B 481 GLU cc_start: 0.8008 (mp0) cc_final: 0.7668 (mp0) REVERT: C 10 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: C 218 SER cc_start: 0.8669 (t) cc_final: 0.8387 (p) REVERT: C 226 MET cc_start: 0.7917 (ttp) cc_final: 0.7669 (ttp) REVERT: C 227 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 358 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: C 385 LEU cc_start: 0.8572 (mp) cc_final: 0.8259 (mm) REVERT: C 407 ASP cc_start: 0.8074 (t0) cc_final: 0.7837 (t0) REVERT: C 482 LEU cc_start: 0.7987 (mt) cc_final: 0.7606 (mt) REVERT: C 486 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8118 (mt) outliers start: 45 outliers final: 34 residues processed: 315 average time/residue: 0.2585 time to fit residues: 110.2958 Evaluate side-chains 330 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 6 PHE Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 0.0030 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 146 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 231 GLN C 393 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.145346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.129428 restraints weight = 25548.443| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.00 r_work: 0.3726 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11125 Z= 0.137 Angle : 0.643 13.074 15137 Z= 0.327 Chirality : 0.042 0.364 1872 Planarity : 0.004 0.059 1935 Dihedral : 4.023 19.531 1565 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.19 % Allowed : 30.36 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.23), residues: 1466 helix: 2.01 (0.17), residues: 990 sheet: 0.14 (0.69), residues: 66 loop : -1.22 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 PHE 0.019 0.001 PHE B 696 TYR 0.023 0.001 TYR C 104 ARG 0.005 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 776) hydrogen bonds : angle 4.46321 ( 2286) covalent geometry : bond 0.00305 (11125) covalent geometry : angle 0.64262 (15137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: A 92 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8379 (ttmm) REVERT: A 114 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: B 67 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7750 (mmt90) REVERT: B 251 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7890 (ttm-80) REVERT: B 293 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8454 (mt) REVERT: B 318 SER cc_start: 0.8438 (m) cc_final: 0.8082 (p) REVERT: B 370 ASN cc_start: 0.8802 (m-40) cc_final: 0.8490 (m110) REVERT: B 481 GLU cc_start: 0.7993 (mp0) cc_final: 0.7684 (mp0) REVERT: C 10 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: C 218 SER cc_start: 0.8670 (t) cc_final: 0.8384 (p) REVERT: C 226 MET cc_start: 0.7858 (ttp) cc_final: 0.7629 (ttp) REVERT: C 227 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 385 LEU cc_start: 0.8579 (mp) cc_final: 0.8262 (mm) REVERT: C 407 ASP cc_start: 0.8055 (t0) cc_final: 0.7823 (t0) REVERT: C 440 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8381 (mtpp) REVERT: C 445 GLN cc_start: 0.7907 (mt0) cc_final: 0.7447 (mp10) REVERT: C 486 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8085 (mt) outliers start: 35 outliers final: 24 residues processed: 313 average time/residue: 0.2659 time to fit residues: 112.4871 Evaluate side-chains 320 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 6 PHE Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 138 optimal weight: 0.0470 chunk 3 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 393 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.144532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128565 restraints weight = 25648.998| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.01 r_work: 0.3710 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11125 Z= 0.161 Angle : 0.666 12.881 15137 Z= 0.338 Chirality : 0.042 0.355 1872 Planarity : 0.004 0.057 1935 Dihedral : 4.109 20.415 1565 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.46 % Allowed : 29.72 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.22), residues: 1466 helix: 1.92 (0.17), residues: 989 sheet: 0.15 (0.69), residues: 66 loop : -1.29 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 PHE 0.018 0.001 PHE D 219 TYR 0.024 0.001 TYR C 104 ARG 0.007 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 776) hydrogen bonds : angle 4.54693 ( 2286) covalent geometry : bond 0.00365 (11125) covalent geometry : angle 0.66569 (15137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9108.24 seconds wall clock time: 158 minutes 19.79 seconds (9499.79 seconds total)