Starting phenix.real_space_refine on Sat Oct 11 02:41:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qfc_18381/10_2025/8qfc_18381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qfc_18381/10_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_18381/10_2025/8qfc_18381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qfc_18381/10_2025/8qfc_18381.map" model { file = "/net/cci-nas-00/data/ceres_data/8qfc_18381/10_2025/8qfc_18381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qfc_18381/10_2025/8qfc_18381.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'GLN:plan1': 2, '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: {'GLU:plan': 23, 'ARG:plan': 6, 'GLN:plan1': 7, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1} 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, 'ASP:plan': 1, 'TYR: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: {'ARG:plan': 14, 'GLU:plan': 34, 'GLN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'PHE:plan': 1} 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: 2.89, per 1000 atoms: 0.26 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: 1.10 Conformation dependent library (CDL) restraints added in 529.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.32 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: 1.80 Time building geometry restraints manager: 1.45 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: 20.550 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.005 0.000 ARG B 660 TYR 0.014 0.001 TYR B 146 PHE 0.014 0.001 PHE B 476 TRP 0.008 0.001 TRP A 198 HIS 0.010 0.001 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00391 (11125) covalent geometry : angle 0.56636 (15137) hydrogen bonds : bond 0.15169 ( 776) hydrogen bonds : angle 6.07494 ( 2286) *********************** 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 : 0.425 Fit side-chains 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: 0.1302 time to fit residues: 54.6420 Evaluate side-chains 306 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0370 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.143772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127875 restraints weight = 25732.832| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.97 r_work: 0.3696 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11125 Z= 0.203 Angle : 0.628 10.342 15137 Z= 0.329 Chirality : 0.043 0.214 1872 Planarity : 0.005 0.073 1935 Dihedral : 4.403 22.073 1565 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.01 % Allowed : 24.16 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.22), residues: 1466 helix: 1.56 (0.16), residues: 983 sheet: -0.23 (0.67), residues: 66 loop : -1.56 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 552 TYR 0.018 0.001 TYR C 104 PHE 0.034 0.002 PHE B 696 TRP 0.010 0.001 TRP A 198 HIS 0.008 0.002 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00450 (11125) covalent geometry : angle 0.62776 (15137) hydrogen bonds : bond 0.05036 ( 776) hydrogen bonds : angle 5.06133 ( 2286) *********************** 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 346 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 0.464 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: 0.8441 (m-30) cc_final: 0.7933 (m-30) REVERT: A 72 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: A 92 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8462 (ttmm) REVERT: B 81 ASP cc_start: 0.7708 (t0) cc_final: 0.7427 (t0) REVERT: B 318 SER cc_start: 0.8580 (m) cc_final: 0.8239 (p) REVERT: B 370 ASN cc_start: 0.8853 (m-40) cc_final: 0.8572 (m110) REVERT: C 226 MET cc_start: 0.7947 (ttm) cc_final: 0.7707 (ttp) REVERT: C 379 SER cc_start: 0.8620 (m) cc_final: 0.8280 (m) REVERT: C 385 LEU cc_start: 0.8540 (mp) cc_final: 0.8227 (mm) REVERT: C 445 GLN cc_start: 0.7945 (mt0) cc_final: 0.7529 (mp10) REVERT: C 482 LEU cc_start: 0.8059 (mt) cc_final: 0.7852 (mt) REVERT: D 247 ASN cc_start: 0.8111 (m-40) cc_final: 0.7830 (m110) outliers start: 44 outliers final: 21 residues processed: 326 average time/residue: 0.1241 time to fit residues: 54.8772 Evaluate side-chains 307 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 359 SER Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 636 GLU 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 D residue 276 LEU 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 8 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.143287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.127365 restraints weight = 25970.489| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.00 r_work: 0.3688 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11125 Z= 0.206 Angle : 0.607 10.455 15137 Z= 0.320 Chirality : 0.042 0.178 1872 Planarity : 0.004 0.055 1935 Dihedral : 4.399 21.538 1565 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.65 % Allowed : 24.07 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1466 helix: 1.58 (0.16), residues: 985 sheet: -0.11 (0.67), residues: 66 loop : -1.45 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 231 TYR 0.017 0.001 TYR C 104 PHE 0.043 0.002 PHE B 696 TRP 0.009 0.001 TRP A 198 HIS 0.008 0.002 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00459 (11125) covalent geometry : angle 0.60695 (15137) hydrogen bonds : bond 0.04989 ( 776) hydrogen bonds : angle 4.87752 ( 2286) *********************** 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 353 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 291 time to evaluate : 0.435 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 46 ASP cc_start: 0.8440 (m-30) cc_final: 0.8075 (m-30) REVERT: A 72 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: A 92 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8443 (ttmm) REVERT: A 114 GLU cc_start: 0.8087 (pm20) cc_final: 0.7819 (mp0) REVERT: B 67 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7724 (mmt90) REVERT: B 293 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8479 (mt) REVERT: B 318 SER cc_start: 0.8542 (m) cc_final: 0.8187 (p) REVERT: B 370 ASN cc_start: 0.8856 (m-40) cc_final: 0.8550 (m110) REVERT: C 226 MET cc_start: 0.8020 (ttm) cc_final: 0.7751 (ttp) REVERT: C 385 LEU cc_start: 0.8541 (mp) cc_final: 0.8241 (mm) REVERT: C 445 GLN cc_start: 0.7947 (mt0) cc_final: 0.7544 (mp10) REVERT: D 243 GLN cc_start: 0.8506 (tp40) cc_final: 0.8280 (tp40) REVERT: D 247 ASN cc_start: 0.8130 (m-40) cc_final: 0.7783 (m-40) outliers start: 62 outliers final: 38 residues processed: 323 average time/residue: 0.1215 time to fit residues: 53.5011 Evaluate side-chains 327 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 196 LYS 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 168 HIS 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 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 B residue 639 ILE Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 91 SER 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 276 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 16 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 70 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 132 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 308 GLN 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 = 0.144371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128382 restraints weight = 25696.149| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.96 r_work: 0.3708 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11125 Z= 0.157 Angle : 0.579 11.212 15137 Z= 0.300 Chirality : 0.041 0.166 1872 Planarity : 0.004 0.053 1935 Dihedral : 4.257 19.998 1565 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.92 % Allowed : 26.44 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.22), residues: 1466 helix: 1.75 (0.17), residues: 983 sheet: 0.11 (0.68), residues: 66 loop : -1.34 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.018 0.001 TYR C 104 PHE 0.033 0.001 PHE B 696 TRP 0.009 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00345 (11125) covalent geometry : angle 0.57915 (15137) hydrogen bonds : bond 0.04461 ( 776) hydrogen bonds : angle 4.67024 ( 2286) *********************** 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 348 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 0.424 Fit side-chains 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: 0.7966 (tt0) REVERT: A 92 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8429 (ttmm) REVERT: A 114 GLU cc_start: 0.8085 (pm20) cc_final: 0.7877 (mp0) REVERT: B 67 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7752 (mmt90) REVERT: B 293 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 318 SER cc_start: 0.8514 (m) cc_final: 0.8150 (p) REVERT: B 370 ASN cc_start: 0.8824 (m-40) cc_final: 0.8510 (m110) REVERT: B 481 GLU cc_start: 0.8127 (mp0) cc_final: 0.7837 (mp0) REVERT: C 226 MET cc_start: 0.7957 (ttm) cc_final: 0.7685 (ttp) REVERT: C 385 LEU cc_start: 0.8545 (mp) cc_final: 0.8252 (mm) REVERT: C 445 GLN cc_start: 0.7917 (mt0) cc_final: 0.7421 (mp10) REVERT: C 489 ASP cc_start: 0.7995 (t0) cc_final: 0.7185 (t0) REVERT: D 237 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8288 (mm110) REVERT: D 243 GLN cc_start: 0.8507 (tp40) cc_final: 0.8239 (tp40) REVERT: D 247 ASN cc_start: 0.8144 (m-40) cc_final: 0.7749 (m110) outliers start: 54 outliers final: 34 residues processed: 326 average time/residue: 0.1164 time to fit residues: 51.9859 Evaluate side-chains 328 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 130 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 128 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 184 HIS B 95 ASN B 113 GLN B 132 GLN B 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.142652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126838 restraints weight = 25734.528| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.96 r_work: 0.3687 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11125 Z= 0.223 Angle : 0.630 11.715 15137 Z= 0.329 Chirality : 0.043 0.239 1872 Planarity : 0.004 0.055 1935 Dihedral : 4.400 21.614 1565 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.02 % Allowed : 26.62 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.22), residues: 1466 helix: 1.61 (0.17), residues: 984 sheet: -0.04 (0.67), residues: 66 loop : -1.43 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 552 TYR 0.020 0.002 TYR E 18 PHE 0.030 0.002 PHE B 696 TRP 0.010 0.001 TRP C 19 HIS 0.010 0.002 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00499 (11125) covalent geometry : angle 0.62969 (15137) hydrogen bonds : bond 0.04860 ( 776) hydrogen bonds : angle 4.79810 ( 2286) *********************** 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 361 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 92 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8448 (ttmm) REVERT: A 114 GLU cc_start: 0.8082 (pm20) cc_final: 0.7796 (mp0) REVERT: B 67 ARG cc_start: 0.8087 (mmt90) cc_final: 0.7803 (mmt90) REVERT: B 129 ASP cc_start: 0.7863 (m-30) cc_final: 0.7641 (m-30) REVERT: B 251 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: B 293 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8474 (mt) REVERT: B 318 SER cc_start: 0.8531 (m) cc_final: 0.8222 (p) REVERT: B 370 ASN cc_start: 0.8833 (m-40) cc_final: 0.8512 (m110) REVERT: B 479 GLN cc_start: 0.8212 (pm20) cc_final: 0.7998 (pm20) REVERT: C 227 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8078 (mp) REVERT: C 385 LEU cc_start: 0.8566 (mp) cc_final: 0.8255 (mm) REVERT: C 445 GLN cc_start: 0.7988 (mt0) cc_final: 0.7542 (mp10) REVERT: C 493 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7278 (mmt90) REVERT: D 237 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8301 (mm110) REVERT: D 243 GLN cc_start: 0.8560 (tp40) cc_final: 0.8295 (tp40) REVERT: D 247 ASN cc_start: 0.8211 (m-40) cc_final: 0.7836 (m110) outliers start: 66 outliers final: 49 residues processed: 335 average time/residue: 0.1187 time to fit residues: 54.1315 Evaluate side-chains 348 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 A residue 196 LYS 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 168 HIS Chi-restraints excluded: chain B residue 208 SER 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 350 SER 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 661 GLU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 91 SER 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 176 ARG Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 389 ILE 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 441 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 8 ILE Chi-restraints excluded: chain E residue 16 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 8 optimal weight: 0.0070 chunk 114 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 C 393 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.128805 restraints weight = 25806.781| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.03 r_work: 0.3717 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11125 Z= 0.127 Angle : 0.599 11.805 15137 Z= 0.303 Chirality : 0.041 0.328 1872 Planarity : 0.004 0.052 1935 Dihedral : 4.198 19.336 1565 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.47 % Allowed : 29.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.22), residues: 1466 helix: 1.83 (0.17), residues: 984 sheet: 0.12 (0.67), residues: 66 loop : -1.33 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.015 0.001 TYR E 18 PHE 0.026 0.001 PHE B 696 TRP 0.011 0.001 TRP C 241 HIS 0.010 0.001 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00273 (11125) covalent geometry : angle 0.59872 (15137) hydrogen bonds : bond 0.04112 ( 776) hydrogen bonds : angle 4.55425 ( 2286) *********************** 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 341 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 92 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8401 (ttmm) REVERT: B 67 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7766 (mmt90) REVERT: B 251 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: B 293 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8451 (mt) REVERT: B 318 SER cc_start: 0.8473 (m) cc_final: 0.8129 (p) REVERT: B 370 ASN cc_start: 0.8800 (m-40) cc_final: 0.8487 (m110) REVERT: B 481 GLU cc_start: 0.8069 (mp0) cc_final: 0.7724 (mp0) REVERT: C 10 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: C 218 SER cc_start: 0.8659 (t) cc_final: 0.8353 (p) REVERT: C 227 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8013 (mp) REVERT: C 385 LEU cc_start: 0.8561 (mp) cc_final: 0.8260 (mm) REVERT: C 407 ASP cc_start: 0.8040 (t0) cc_final: 0.7753 (t0) REVERT: C 445 GLN cc_start: 0.7979 (mt0) cc_final: 0.7524 (mp10) REVERT: C 489 ASP cc_start: 0.7901 (t0) cc_final: 0.7605 (t0) REVERT: C 493 ARG cc_start: 0.7814 (mmt90) cc_final: 0.7514 (mmt90) REVERT: D 237 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8279 (mm110) REVERT: D 243 GLN cc_start: 0.8557 (tp40) cc_final: 0.8256 (tp40) REVERT: D 247 ASN cc_start: 0.8150 (m-40) cc_final: 0.7724 (m110) outliers start: 49 outliers final: 32 residues processed: 317 average time/residue: 0.1184 time to fit residues: 51.1339 Evaluate side-chains 325 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 208 SER 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 509 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 661 GLU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 686 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 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 D residue 197 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 25 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 B 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.142839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126957 restraints weight = 25798.760| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.98 r_work: 0.3687 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11125 Z= 0.207 Angle : 0.631 11.985 15137 Z= 0.328 Chirality : 0.043 0.313 1872 Planarity : 0.004 0.053 1935 Dihedral : 4.356 21.385 1565 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.74 % Allowed : 28.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.22), residues: 1466 helix: 1.67 (0.17), residues: 983 sheet: -0.18 (0.68), residues: 64 loop : -1.38 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 231 TYR 0.019 0.001 TYR E 18 PHE 0.024 0.002 PHE B 696 TRP 0.008 0.001 TRP A 198 HIS 0.010 0.002 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00466 (11125) covalent geometry : angle 0.63128 (15137) hydrogen bonds : bond 0.04667 ( 776) hydrogen bonds : angle 4.75690 ( 2286) *********************** 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 348 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.356 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: 0.8714 (ttmm) cc_final: 0.8431 (ttmm) REVERT: B 67 ARG cc_start: 0.8096 (mmt90) cc_final: 0.7768 (mmt90) REVERT: B 251 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: B 293 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8480 (mt) REVERT: B 318 SER cc_start: 0.8509 (m) cc_final: 0.8198 (p) REVERT: B 370 ASN cc_start: 0.8830 (m-40) cc_final: 0.8519 (m110) REVERT: C 218 SER cc_start: 0.8673 (t) cc_final: 0.8383 (p) REVERT: C 226 MET cc_start: 0.7843 (ttm) cc_final: 0.7634 (ttp) REVERT: C 227 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 385 LEU cc_start: 0.8570 (mp) cc_final: 0.8250 (mm) REVERT: C 445 GLN cc_start: 0.8000 (mt0) cc_final: 0.7563 (mp10) REVERT: C 489 ASP cc_start: 0.7889 (t0) cc_final: 0.7495 (t0) REVERT: C 493 ARG cc_start: 0.7884 (mmt90) cc_final: 0.7562 (mmt90) REVERT: D 237 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8300 (mm110) REVERT: D 243 GLN cc_start: 0.8568 (tp40) cc_final: 0.8211 (tp40) REVERT: D 247 ASN cc_start: 0.8161 (m-40) cc_final: 0.7683 (m110) outliers start: 52 outliers final: 36 residues processed: 329 average time/residue: 0.1199 time to fit residues: 53.6560 Evaluate side-chains 333 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 94 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 208 SER 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 350 SER 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 661 GLU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 686 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 227 LEU Chi-restraints excluded: chain C residue 389 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 105 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 81 optimal weight: 0.0970 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 132 GLN B 308 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 = 0.4103 r_free = 0.4103 target = 0.145402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.129471 restraints weight = 25725.819| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.01 r_work: 0.3727 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2723 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= 0.121 Angle : 0.598 12.588 15137 Z= 0.302 Chirality : 0.040 0.340 1872 Planarity : 0.004 0.056 1935 Dihedral : 4.110 20.105 1565 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.46 % Allowed : 29.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.22), residues: 1466 helix: 1.92 (0.17), residues: 986 sheet: 0.11 (0.68), residues: 66 loop : -1.18 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 286 TYR 0.008 0.001 TYR C 110 PHE 0.021 0.001 PHE B 696 TRP 0.008 0.001 TRP C 19 HIS 0.010 0.001 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00261 (11125) covalent geometry : angle 0.59783 (15137) hydrogen bonds : bond 0.03857 ( 776) hydrogen bonds : angle 4.47535 ( 2286) *********************** 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 329 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: A 92 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8381 (ttmm) REVERT: B 52 ASP cc_start: 0.7866 (t70) cc_final: 0.7134 (t0) REVERT: B 67 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7720 (mmt90) REVERT: B 251 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: B 293 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 318 SER cc_start: 0.8425 (m) cc_final: 0.8086 (p) REVERT: B 370 ASN cc_start: 0.8791 (m-40) cc_final: 0.8472 (m110) REVERT: B 481 GLU cc_start: 0.7930 (mp0) cc_final: 0.7638 (mp0) REVERT: C 218 SER cc_start: 0.8656 (t) cc_final: 0.8355 (p) REVERT: C 227 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8047 (mp) REVERT: C 385 LEU cc_start: 0.8566 (mp) cc_final: 0.8258 (mm) REVERT: C 407 ASP cc_start: 0.8036 (t0) cc_final: 0.7752 (t0) REVERT: C 445 GLN cc_start: 0.7980 (mt0) cc_final: 0.7780 (mt0) REVERT: C 494 TYR cc_start: 0.7635 (m-10) cc_final: 0.7377 (m-10) REVERT: D 243 GLN cc_start: 0.8566 (tp40) cc_final: 0.8185 (tp40) REVERT: D 247 ASN cc_start: 0.8126 (m-40) cc_final: 0.7647 (m110) outliers start: 38 outliers final: 27 residues processed: 312 average time/residue: 0.1254 time to fit residues: 52.7588 Evaluate side-chains 318 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 208 SER 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 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 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 406 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 472 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 28 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.0970 chunk 44 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 308 GLN C 231 GLN D 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129769 restraints weight = 25525.677| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.98 r_work: 0.3731 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11125 Z= 0.124 Angle : 0.609 12.893 15137 Z= 0.308 Chirality : 0.041 0.352 1872 Planarity : 0.004 0.057 1935 Dihedral : 4.016 18.888 1565 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.65 % Allowed : 30.36 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.22), residues: 1466 helix: 1.98 (0.17), residues: 986 sheet: -0.13 (0.62), residues: 76 loop : -1.10 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.014 0.001 TYR E 18 PHE 0.025 0.001 PHE E 67 TRP 0.021 0.001 TRP C 241 HIS 0.011 0.001 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00273 (11125) covalent geometry : angle 0.60937 (15137) hydrogen bonds : bond 0.03824 ( 776) hydrogen bonds : angle 4.41811 ( 2286) *********************** 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 320 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 92 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8396 (ttmm) REVERT: B 52 ASP cc_start: 0.7874 (t70) cc_final: 0.7260 (t0) REVERT: B 67 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7807 (mmt90) REVERT: B 251 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: B 293 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8450 (mt) REVERT: B 370 ASN cc_start: 0.8790 (m-40) cc_final: 0.8474 (m110) REVERT: B 481 GLU cc_start: 0.7915 (mp0) cc_final: 0.7642 (mp0) REVERT: C 218 SER cc_start: 0.8653 (t) cc_final: 0.8361 (p) REVERT: C 385 LEU cc_start: 0.8577 (mp) cc_final: 0.8269 (mm) REVERT: C 407 ASP cc_start: 0.7995 (t0) cc_final: 0.7728 (t0) REVERT: C 440 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8425 (mtpp) REVERT: C 489 ASP cc_start: 0.7833 (t0) cc_final: 0.7359 (t0) REVERT: C 493 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7531 (mmt90) REVERT: C 494 TYR cc_start: 0.7563 (m-10) cc_final: 0.7333 (m-10) REVERT: D 243 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8164 (tp40) REVERT: D 247 ASN cc_start: 0.8071 (m-40) cc_final: 0.7497 (m-40) outliers start: 40 outliers final: 32 residues processed: 305 average time/residue: 0.1190 time to fit residues: 49.7266 Evaluate side-chains 317 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS 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 100 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 208 SER 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 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 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 406 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 220 ILE 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 126 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.144999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129037 restraints weight = 25508.560| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.92 r_work: 0.3717 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11125 Z= 0.158 Angle : 0.643 12.946 15137 Z= 0.328 Chirality : 0.042 0.355 1872 Planarity : 0.004 0.059 1935 Dihedral : 4.104 20.689 1565 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.83 % Allowed : 30.08 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.22), residues: 1466 helix: 1.94 (0.17), residues: 984 sheet: 0.09 (0.69), residues: 66 loop : -1.20 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 24 TYR 0.022 0.001 TYR E 18 PHE 0.020 0.001 PHE B 476 TRP 0.007 0.001 TRP C 19 HIS 0.011 0.002 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00358 (11125) covalent geometry : angle 0.64254 (15137) hydrogen bonds : bond 0.04107 ( 776) hydrogen bonds : angle 4.49737 ( 2286) ********************** 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 331 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 0.507 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 41 TYR cc_start: 0.8841 (t80) cc_final: 0.8496 (t80) REVERT: A 72 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 92 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8407 (ttmm) REVERT: B 67 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7817 (mmt90) REVERT: B 251 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7906 (ttm-80) REVERT: B 293 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 318 SER cc_start: 0.8470 (m) cc_final: 0.8120 (p) REVERT: B 370 ASN cc_start: 0.8814 (m-40) cc_final: 0.8512 (m110) REVERT: B 481 GLU cc_start: 0.7919 (mp0) cc_final: 0.7643 (mp0) REVERT: C 218 SER cc_start: 0.8663 (t) cc_final: 0.8383 (p) REVERT: C 227 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (mp) REVERT: C 385 LEU cc_start: 0.8573 (mp) cc_final: 0.8265 (mm) REVERT: C 407 ASP cc_start: 0.8015 (t0) cc_final: 0.7745 (t0) REVERT: C 440 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8404 (mtpp) REVERT: C 494 TYR cc_start: 0.7591 (m-10) cc_final: 0.7331 (m-10) REVERT: D 243 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8134 (tp40) REVERT: D 247 ASN cc_start: 0.8079 (m-40) cc_final: 0.7522 (m110) outliers start: 42 outliers final: 35 residues processed: 316 average time/residue: 0.1259 time to fit residues: 53.7959 Evaluate side-chains 323 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 208 SER 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 350 SER 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 665 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 725 HIS Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 132 GLN 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 406 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 472 LEU 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 25 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.144558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128487 restraints weight = 25447.509| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.95 r_work: 0.3710 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2948 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= 0.162 Angle : 0.657 12.893 15137 Z= 0.333 Chirality : 0.042 0.359 1872 Planarity : 0.004 0.056 1935 Dihedral : 4.216 24.218 1565 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.83 % Allowed : 30.17 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.22), residues: 1466 helix: 1.84 (0.17), residues: 985 sheet: -0.23 (0.68), residues: 66 loop : -1.28 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 24 TYR 0.021 0.001 TYR E 18 PHE 0.019 0.002 PHE B 476 TRP 0.006 0.001 TRP C 19 HIS 0.010 0.002 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.00365 (11125) covalent geometry : angle 0.65723 (15137) hydrogen bonds : bond 0.04191 ( 776) hydrogen bonds : angle 4.56339 ( 2286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4262.67 seconds wall clock time: 73 minutes 13.40 seconds (4393.40 seconds total)