Starting phenix.real_space_refine on Sat Jul 4 20:59:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d4p_30575/07_2026/7d4p_30575.map" } resolution = 2.7 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= 0.010 sd= 0.196 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 Cl 4 4.86 5 C 14756 2.51 5 N 3592 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5438 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 644} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' CA': 1, ' ZN': 1, 'GX0': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1155 SG CYS A 176 98.631 69.677 61.888 1.00147.88 S ATOM 1169 SG CYS A 178 99.979 72.459 59.636 1.00161.95 S ATOM 1191 SG CYS A 181 96.242 71.752 59.728 1.00162.23 S Restraints were copied for chains: B, C, D Time building chain proxies: 5.96, per 1000 atoms: 0.27 Number of scatterers: 22472 At special positions: 0 Unit cell: (113.905, 113.905, 136.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 Cl 4 17.00 S 116 16.00 P 8 15.00 O 3988 8.00 N 3592 7.00 C 14756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.04 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.04 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 176 " pdb=" ZN B 805 " pdb="ZN ZN B 805 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 176 " pdb=" ZN C 805 " pdb="ZN ZN C 805 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 176 " pdb=" ZN D 805 " pdb="ZN ZN D 805 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 176 " Number of angles added : 12 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.9% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.655A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.958A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.561A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 460 removed outlier: 4.145A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.555A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.938A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.666A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.540A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.608A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 734 Processing helix chain 'A' and resid 740 through 762 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.655A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.958A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.562A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 460 removed outlier: 4.145A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.555A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.938A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.666A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.541A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.608A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 734 Processing helix chain 'B' and resid 740 through 762 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.655A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.958A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.561A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 460 removed outlier: 4.145A pdb=" N LEU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.555A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.938A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.666A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.541A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.608A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 734 Processing helix chain 'C' and resid 740 through 762 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.655A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.958A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.562A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 460 removed outlier: 4.145A pdb=" N LEU D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.556A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.938A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.666A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.541A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.609A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 734 Processing helix chain 'D' and resid 740 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.410A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.410A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.410A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.410A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1484 hydrogen bonds defined for protein. 4344 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: 4.05 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3520 1.29 - 1.42: 5964 1.42 - 1.56: 13284 1.56 - 1.69: 16 1.69 - 1.82: 192 Bond restraints: 22976 Sorted by residual: bond pdb=" C12 YZY D 807 " pdb=" C13 YZY D 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY A 807 " pdb=" C13 YZY A 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY C 807 " pdb=" C13 YZY C 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY B 807 " pdb=" C13 YZY B 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C29 YZY A 807 " pdb=" C30 YZY A 807 " ideal model delta sigma weight residual 1.497 1.325 0.172 2.00e-02 2.50e+03 7.44e+01 ... (remaining 22971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 30840 3.86 - 7.72: 148 7.72 - 11.57: 48 11.57 - 15.43: 12 15.43 - 19.29: 4 Bond angle restraints: 31052 Sorted by residual: angle pdb=" C27 YZY C 807 " pdb=" C28 YZY C 807 " pdb=" C29 YZY C 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY A 807 " pdb=" C28 YZY A 807 " pdb=" C29 YZY A 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY D 807 " pdb=" C28 YZY D 807 " pdb=" C29 YZY D 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY B 807 " pdb=" C28 YZY B 807 " pdb=" C29 YZY B 807 " ideal model delta sigma weight residual 128.13 108.85 19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C21 YZY C 807 " pdb=" C20 YZY C 807 " pdb=" O4 YZY C 807 " ideal model delta sigma weight residual 111.77 126.94 -15.17 3.00e+00 1.11e-01 2.56e+01 ... (remaining 31047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.83: 13432 32.83 - 65.67: 232 65.67 - 98.50: 40 98.50 - 131.34: 4 131.34 - 164.17: 8 Dihedral angle restraints: 13716 sinusoidal: 5800 harmonic: 7916 Sorted by residual: dihedral pdb=" C5 YZY D 807 " pdb=" C3 YZY D 807 " pdb=" C4 YZY D 807 " pdb=" O2 YZY D 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.57 164.17 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY B 807 " pdb=" C3 YZY B 807 " pdb=" C4 YZY B 807 " pdb=" O2 YZY B 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.61 164.13 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY A 807 " pdb=" C3 YZY A 807 " pdb=" C4 YZY A 807 " pdb=" O2 YZY A 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.61 164.13 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2866 0.045 - 0.090: 514 0.090 - 0.134: 72 0.134 - 0.179: 8 0.179 - 0.224: 8 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CBI Y01 A 804 " pdb=" CAU Y01 A 804 " pdb=" CBE Y01 A 804 " pdb=" CBG Y01 A 804 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CBI Y01 B 804 " pdb=" CAU Y01 B 804 " pdb=" CBE Y01 B 804 " pdb=" CBG Y01 B 804 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CBI Y01 C 804 " pdb=" CAU Y01 C 804 " pdb=" CBE Y01 C 804 " pdb=" CBG Y01 C 804 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3465 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 442 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C MET C 442 " 0.037 2.00e-02 2.50e+03 pdb=" O MET C 442 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 443 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 441 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ALA B 441 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA B 441 " 0.014 2.00e-02 2.50e+03 pdb=" N MET B 442 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ALA C 441 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA C 441 " -0.014 2.00e-02 2.50e+03 pdb=" N MET C 442 " -0.012 2.00e-02 2.50e+03 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5178 2.79 - 3.32: 22306 3.32 - 3.85: 37950 3.85 - 4.37: 44644 4.37 - 4.90: 76924 Nonbonded interactions: 187002 Sorted by model distance: nonbonded pdb=" OAH Y01 D 804 " pdb=" OAW Y01 D 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 A 804 " pdb=" OAW Y01 A 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 C 804 " pdb=" OAW Y01 C 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 B 804 " pdb=" OAW Y01 B 804 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.290 3.040 ... (remaining 186997 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.670 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.780 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.007 0.215 22996 Z= 0.354 Angle : 0.798 19.289 31072 Z= 0.333 Chirality : 0.036 0.224 3468 Planarity : 0.004 0.032 3812 Dihedral : 13.567 164.170 8552 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.67 % Allowed : 3.36 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.16), residues: 2628 helix: 2.10 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.016 0.001 TYR D 524 PHE 0.015 0.001 PHE A 341 TRP 0.009 0.001 TRP A 315 HIS 0.002 0.000 HIS D 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.35 (22976) covalent geometry : angle 0.79763 / 0.33 (31052) SS BOND : bond 0.00508 / 0.25 ( 4) SS BOND : angle 0.76098 / 0.49 ( 8) hydrogen bonds : bond 0.10950 / 7.29 ( 1484) hydrogen bonds : angle 5.06670 / 3.81 ( 4344) metal coordination : bond 0.01136 / 1.13 ( 16) metal coordination : angle 1.33825 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 495 time to evaluate : 0.870 Fit side-chains REVERT: A 222 ARG cc_start: 0.7819 (ptp-170) cc_final: 0.7300 (mtm-85) REVERT: A 238 LYS cc_start: 0.7300 (ttpp) cc_final: 0.6936 (ttmm) REVERT: A 340 LEU cc_start: 0.7638 (mt) cc_final: 0.7307 (tp) REVERT: A 380 MET cc_start: 0.7290 (mtm) cc_final: 0.7011 (mmp) REVERT: A 382 LEU cc_start: 0.7577 (mt) cc_final: 0.7361 (tp) REVERT: A 393 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5537 (mt) REVERT: A 510 LEU cc_start: 0.7150 (mt) cc_final: 0.6604 (tt) REVERT: A 512 ARG cc_start: 0.7413 (tpt90) cc_final: 0.7074 (tpp80) REVERT: A 516 ASP cc_start: 0.6625 (m-30) cc_final: 0.6390 (m-30) REVERT: A 551 ASN cc_start: 0.8348 (t0) cc_final: 0.8028 (t0) REVERT: A 728 MET cc_start: 0.7259 (mmt) cc_final: 0.6945 (mmp) REVERT: A 756 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6412 (mt-10) REVERT: B 222 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7302 (mtm-85) REVERT: B 238 LYS cc_start: 0.7302 (ttpp) cc_final: 0.6939 (ttmm) REVERT: B 340 LEU cc_start: 0.7645 (mt) cc_final: 0.7311 (tp) REVERT: B 380 MET cc_start: 0.7274 (mtm) cc_final: 0.6997 (mmp) REVERT: B 382 LEU cc_start: 0.7565 (mt) cc_final: 0.7345 (tp) REVERT: B 393 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5536 (mt) REVERT: B 510 LEU cc_start: 0.7053 (mt) cc_final: 0.6580 (tt) REVERT: B 512 ARG cc_start: 0.7411 (tpt90) cc_final: 0.7071 (tpp80) REVERT: B 516 ASP cc_start: 0.6596 (m-30) cc_final: 0.6358 (m-30) REVERT: B 570 GLU cc_start: 0.8372 (tp30) cc_final: 0.8172 (mm-30) REVERT: B 728 MET cc_start: 0.7253 (mmt) cc_final: 0.6943 (mmp) REVERT: B 756 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6395 (mt-10) REVERT: C 66 MET cc_start: 0.7712 (mmt) cc_final: 0.7512 (mmm) REVERT: C 222 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7299 (mtm-85) REVERT: C 238 LYS cc_start: 0.7326 (ttpp) cc_final: 0.6972 (ttmm) REVERT: C 340 LEU cc_start: 0.7628 (mt) cc_final: 0.7292 (tp) REVERT: C 380 MET cc_start: 0.7342 (mtm) cc_final: 0.7068 (mmp) REVERT: C 382 LEU cc_start: 0.7563 (mt) cc_final: 0.7352 (tp) REVERT: C 393 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5516 (mt) REVERT: C 510 LEU cc_start: 0.7053 (mt) cc_final: 0.6582 (tt) REVERT: C 512 ARG cc_start: 0.7412 (tpt90) cc_final: 0.7069 (tpp80) REVERT: C 516 ASP cc_start: 0.6592 (m-30) cc_final: 0.6353 (m-30) REVERT: C 551 ASN cc_start: 0.8383 (t0) cc_final: 0.8053 (t0) REVERT: C 728 MET cc_start: 0.7256 (mmt) cc_final: 0.6951 (mmp) REVERT: C 756 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6384 (mt-10) REVERT: D 222 ARG cc_start: 0.7814 (ptp-170) cc_final: 0.7300 (mtm-85) REVERT: D 238 LYS cc_start: 0.7303 (ttpp) cc_final: 0.6939 (ttmm) REVERT: D 340 LEU cc_start: 0.7622 (mt) cc_final: 0.7305 (tp) REVERT: D 380 MET cc_start: 0.7288 (mtm) cc_final: 0.7015 (mmp) REVERT: D 382 LEU cc_start: 0.7573 (mt) cc_final: 0.7357 (tp) REVERT: D 393 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.5580 (mt) REVERT: D 510 LEU cc_start: 0.7056 (mt) cc_final: 0.6585 (tt) REVERT: D 512 ARG cc_start: 0.7413 (tpt90) cc_final: 0.7069 (tpp80) REVERT: D 516 ASP cc_start: 0.6617 (m-30) cc_final: 0.6382 (m-30) REVERT: D 551 ASN cc_start: 0.8426 (t0) cc_final: 0.8088 (t0) REVERT: D 728 MET cc_start: 0.7261 (mmt) cc_final: 0.6951 (mmp) REVERT: D 756 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6407 (mt-10) outliers start: 16 outliers final: 3 residues processed: 511 average time/residue: 0.7008 time to fit residues: 406.0474 Evaluate side-chains 327 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 320 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 517 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 573 GLN A 711 GLN B 247 GLN B 573 GLN B 711 GLN C 247 GLN C 573 GLN C 711 GLN D 247 GLN D 533 ASN D 573 GLN D 711 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116541 restraints weight = 23974.554| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.20 r_work: 0.3253 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22996 Z= 0.113 Angle : 0.479 7.103 31072 Z= 0.239 Chirality : 0.035 0.150 3468 Planarity : 0.004 0.038 3812 Dihedral : 12.876 171.181 3314 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.80 % Allowed : 13.05 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.16), residues: 2628 helix: 2.51 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.33 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.014 0.001 TYR D 348 PHE 0.016 0.001 PHE C 341 TRP 0.012 0.001 TRP C 639 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22976) covalent geometry : angle 0.47846 / 0.24 (31052) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.59219 / 0.38 ( 8) hydrogen bonds : bond 0.04067 / 2.71 ( 1484) hydrogen bonds : angle 3.77529 / 2.79 ( 4344) metal coordination : bond 0.00487 / 0.44 ( 16) metal coordination : angle 1.35001 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7987 (mmm) cc_final: 0.7678 (mmm) REVERT: A 79 GLU cc_start: 0.8087 (tt0) cc_final: 0.7040 (mm-30) REVERT: A 222 ARG cc_start: 0.7881 (ptp-170) cc_final: 0.7352 (mtm-85) REVERT: A 238 LYS cc_start: 0.7154 (ttpp) cc_final: 0.6801 (ttmm) REVERT: A 257 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: A 340 LEU cc_start: 0.7482 (mt) cc_final: 0.7082 (tp) REVERT: A 343 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7170 (ttm) REVERT: A 380 MET cc_start: 0.7303 (mtm) cc_final: 0.7020 (mmp) REVERT: A 393 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5423 (mt) REVERT: A 512 ARG cc_start: 0.7344 (tpt90) cc_final: 0.7128 (tpp80) REVERT: A 516 ASP cc_start: 0.6648 (m-30) cc_final: 0.6442 (m-30) REVERT: A 551 ASN cc_start: 0.8395 (t0) cc_final: 0.8078 (t0) REVERT: A 744 LYS cc_start: 0.7254 (tptt) cc_final: 0.6946 (tptp) REVERT: A 756 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6399 (mt-10) REVERT: A 760 LEU cc_start: 0.7734 (mp) cc_final: 0.7373 (mp) REVERT: B 66 MET cc_start: 0.7965 (mmm) cc_final: 0.7654 (mmm) REVERT: B 79 GLU cc_start: 0.8048 (tt0) cc_final: 0.7024 (mm-30) REVERT: B 222 ARG cc_start: 0.7877 (ptp-170) cc_final: 0.7349 (mtm-85) REVERT: B 238 LYS cc_start: 0.7167 (ttpp) cc_final: 0.6813 (ttmm) REVERT: B 257 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: B 340 LEU cc_start: 0.7465 (mt) cc_final: 0.7064 (tp) REVERT: B 343 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7166 (ttm) REVERT: B 380 MET cc_start: 0.7312 (mtm) cc_final: 0.7030 (mmp) REVERT: B 393 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5435 (mt) REVERT: B 512 ARG cc_start: 0.7357 (tpt90) cc_final: 0.7127 (tpp80) REVERT: B 551 ASN cc_start: 0.8418 (t0) cc_final: 0.8068 (t0) REVERT: B 570 GLU cc_start: 0.8530 (tp30) cc_final: 0.8205 (mm-30) REVERT: B 744 LYS cc_start: 0.7268 (tptt) cc_final: 0.6965 (tptp) REVERT: B 756 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6406 (mt-10) REVERT: B 760 LEU cc_start: 0.7764 (mp) cc_final: 0.7407 (mp) REVERT: C 79 GLU cc_start: 0.8057 (tt0) cc_final: 0.7060 (mm-30) REVERT: C 222 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.7365 (mtm-85) REVERT: C 238 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6796 (ttmm) REVERT: C 257 ASP cc_start: 0.7986 (m-30) cc_final: 0.7741 (m-30) REVERT: C 340 LEU cc_start: 0.7385 (mt) cc_final: 0.7050 (tp) REVERT: C 343 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7104 (ttm) REVERT: C 361 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7447 (mtmm) REVERT: C 380 MET cc_start: 0.7325 (mtm) cc_final: 0.7044 (mmp) REVERT: C 393 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5421 (mt) REVERT: C 512 ARG cc_start: 0.7381 (tpt90) cc_final: 0.7144 (tpp80) REVERT: C 551 ASN cc_start: 0.8398 (t0) cc_final: 0.8065 (t0) REVERT: C 728 MET cc_start: 0.7226 (mmt) cc_final: 0.6794 (mmp) REVERT: C 744 LYS cc_start: 0.7250 (tptt) cc_final: 0.6948 (tptp) REVERT: C 756 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6376 (mt-10) REVERT: C 760 LEU cc_start: 0.7759 (mp) cc_final: 0.7408 (mp) REVERT: D 66 MET cc_start: 0.7975 (mmm) cc_final: 0.7667 (mmm) REVERT: D 79 GLU cc_start: 0.8096 (tt0) cc_final: 0.7078 (mm-30) REVERT: D 222 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7355 (mtm-85) REVERT: D 238 LYS cc_start: 0.7159 (ttpp) cc_final: 0.6803 (ttmm) REVERT: D 257 ASP cc_start: 0.7996 (m-30) cc_final: 0.7748 (m-30) REVERT: D 340 LEU cc_start: 0.7400 (mt) cc_final: 0.7082 (tp) REVERT: D 343 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7145 (ttm) REVERT: D 361 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7485 (mtmm) REVERT: D 380 MET cc_start: 0.7309 (mtm) cc_final: 0.7030 (mmp) REVERT: D 393 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5456 (mt) REVERT: D 512 ARG cc_start: 0.7355 (tpt90) cc_final: 0.7137 (tpp80) REVERT: D 551 ASN cc_start: 0.8480 (t0) cc_final: 0.8150 (t0) REVERT: D 744 LYS cc_start: 0.7242 (tptt) cc_final: 0.6939 (tptp) REVERT: D 756 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6432 (mt-10) REVERT: D 760 LEU cc_start: 0.7726 (mp) cc_final: 0.7385 (mp) outliers start: 43 outliers final: 4 residues processed: 345 average time/residue: 0.6396 time to fit residues: 251.7127 Evaluate side-chains 304 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 4 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 210 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 GLN B 711 GLN C 711 GLN D 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114249 restraints weight = 23958.499| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.19 r_work: 0.3220 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22996 Z= 0.138 Angle : 0.467 7.222 31072 Z= 0.236 Chirality : 0.035 0.147 3468 Planarity : 0.004 0.044 3812 Dihedral : 12.105 169.086 3308 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.89 % Allowed : 13.30 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.16), residues: 2628 helix: 2.48 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.19 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 191 TYR 0.019 0.001 TYR C 348 PHE 0.016 0.002 PHE B 520 TRP 0.013 0.001 TRP D 315 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (22976) covalent geometry : angle 0.46652 / 0.24 (31052) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 0.57643 / 0.37 ( 8) hydrogen bonds : bond 0.04202 / 2.81 ( 1484) hydrogen bonds : angle 3.67600 / 2.70 ( 4344) metal coordination : bond 0.00348 / 0.28 ( 16) metal coordination : angle 0.82914 / 0.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 309 time to evaluate : 0.909 Fit side-chains REVERT: A 66 MET cc_start: 0.8010 (mmm) cc_final: 0.7779 (mmm) REVERT: A 79 GLU cc_start: 0.7989 (tt0) cc_final: 0.6954 (mm-30) REVERT: A 170 ARG cc_start: 0.7880 (ttm170) cc_final: 0.6589 (pmt170) REVERT: A 222 ARG cc_start: 0.7979 (ptp-170) cc_final: 0.7466 (mtm-85) REVERT: A 238 LYS cc_start: 0.7334 (ttpp) cc_final: 0.6984 (ttmm) REVERT: A 257 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: A 331 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7004 (tm) REVERT: A 343 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7364 (ttm) REVERT: A 361 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7690 (tttt) REVERT: A 380 MET cc_start: 0.7423 (mtm) cc_final: 0.7137 (mmp) REVERT: A 382 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 393 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5461 (mt) REVERT: A 512 ARG cc_start: 0.7573 (tpt90) cc_final: 0.7224 (tpp80) REVERT: A 516 ASP cc_start: 0.6881 (m-30) cc_final: 0.6664 (m-30) REVERT: A 551 ASN cc_start: 0.8482 (t0) cc_final: 0.8093 (t0) REVERT: A 728 MET cc_start: 0.7232 (mmt) cc_final: 0.6759 (mmp) REVERT: A 756 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6593 (mt-10) REVERT: B 66 MET cc_start: 0.7913 (mmm) cc_final: 0.7684 (mmm) REVERT: B 79 GLU cc_start: 0.8018 (tt0) cc_final: 0.6984 (mm-30) REVERT: B 170 ARG cc_start: 0.7883 (ttm170) cc_final: 0.6591 (pmt170) REVERT: B 222 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7467 (mtm-85) REVERT: B 238 LYS cc_start: 0.7333 (ttpp) cc_final: 0.6984 (ttmm) REVERT: B 257 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: B 331 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7028 (tm) REVERT: B 343 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7361 (ttm) REVERT: B 380 MET cc_start: 0.7484 (mtm) cc_final: 0.7190 (mmp) REVERT: B 382 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 393 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5483 (mt) REVERT: B 512 ARG cc_start: 0.7570 (tpt90) cc_final: 0.7192 (tpp80) REVERT: B 551 ASN cc_start: 0.8399 (t0) cc_final: 0.8009 (t0) REVERT: B 570 GLU cc_start: 0.8602 (tp30) cc_final: 0.8358 (mm-30) REVERT: B 728 MET cc_start: 0.7249 (mmt) cc_final: 0.6776 (mmp) REVERT: B 756 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6645 (mt-10) REVERT: C 79 GLU cc_start: 0.8000 (tt0) cc_final: 0.6999 (mm-30) REVERT: C 170 ARG cc_start: 0.7893 (ttm170) cc_final: 0.6594 (pmt170) REVERT: C 222 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7472 (mtm-85) REVERT: C 238 LYS cc_start: 0.7339 (ttpp) cc_final: 0.6989 (ttmm) REVERT: C 257 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: C 343 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7363 (ttm) REVERT: C 361 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7799 (tttt) REVERT: C 380 MET cc_start: 0.7443 (mtm) cc_final: 0.7154 (mmp) REVERT: C 382 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7481 (mp) REVERT: C 393 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5458 (mt) REVERT: C 512 ARG cc_start: 0.7567 (tpt90) cc_final: 0.7197 (tpp80) REVERT: C 551 ASN cc_start: 0.8405 (t0) cc_final: 0.8010 (t0) REVERT: C 728 MET cc_start: 0.7285 (mmt) cc_final: 0.6888 (mmp) REVERT: C 756 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6539 (mt-10) REVERT: C 760 LEU cc_start: 0.7785 (mp) cc_final: 0.7427 (mp) REVERT: D 66 MET cc_start: 0.8010 (mmm) cc_final: 0.7764 (mmm) REVERT: D 79 GLU cc_start: 0.8014 (tt0) cc_final: 0.7015 (mm-30) REVERT: D 170 ARG cc_start: 0.7871 (ttm170) cc_final: 0.6584 (pmt170) REVERT: D 222 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7471 (mtm-85) REVERT: D 238 LYS cc_start: 0.7318 (ttpp) cc_final: 0.6968 (ttmm) REVERT: D 257 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: D 343 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7404 (ttm) REVERT: D 361 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7740 (tttt) REVERT: D 380 MET cc_start: 0.7432 (mtm) cc_final: 0.7142 (mmp) REVERT: D 382 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7507 (mp) REVERT: D 393 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5461 (mt) REVERT: D 512 ARG cc_start: 0.7567 (tpt90) cc_final: 0.7192 (tpp80) REVERT: D 551 ASN cc_start: 0.8483 (t0) cc_final: 0.8091 (t0) REVERT: D 728 MET cc_start: 0.7228 (mmt) cc_final: 0.6753 (mmp) REVERT: D 756 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6641 (mt-10) outliers start: 69 outliers final: 13 residues processed: 347 average time/residue: 0.6237 time to fit residues: 248.5647 Evaluate side-chains 322 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 98 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114686 restraints weight = 24068.973| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.20 r_work: 0.3226 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22996 Z= 0.126 Angle : 0.451 7.508 31072 Z= 0.227 Chirality : 0.035 0.150 3468 Planarity : 0.004 0.046 3812 Dihedral : 11.322 153.339 3308 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.27 % Allowed : 14.56 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.16), residues: 2628 helix: 2.48 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : 0.10 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 191 TYR 0.015 0.001 TYR C 348 PHE 0.014 0.001 PHE A 341 TRP 0.015 0.001 TRP B 315 HIS 0.002 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (22976) covalent geometry : angle 0.45063 / 0.23 (31052) SS BOND : bond 0.00163 / 0.08 ( 4) SS BOND : angle 0.50927 / 0.34 ( 8) hydrogen bonds : bond 0.04009 / 2.68 ( 1484) hydrogen bonds : angle 3.61491 / 2.65 ( 4344) metal coordination : bond 0.00322 / 0.28 ( 16) metal coordination : angle 0.52856 / 0.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7896 (tt0) cc_final: 0.6929 (mm-30) REVERT: A 222 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.7547 (mtm-85) REVERT: A 238 LYS cc_start: 0.7249 (ttpp) cc_final: 0.6920 (ttmm) REVERT: A 257 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 331 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6984 (tm) REVERT: A 380 MET cc_start: 0.7645 (mtm) cc_final: 0.7258 (mmp) REVERT: A 382 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 393 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5409 (mt) REVERT: A 422 MET cc_start: 0.7512 (tpp) cc_final: 0.6688 (ttp) REVERT: A 512 ARG cc_start: 0.7594 (tpt90) cc_final: 0.7221 (tpp80) REVERT: A 516 ASP cc_start: 0.6594 (m-30) cc_final: 0.6380 (m-30) REVERT: A 529 LEU cc_start: 0.8080 (tp) cc_final: 0.7797 (mt) REVERT: A 551 ASN cc_start: 0.8451 (t0) cc_final: 0.8063 (t0) REVERT: A 728 MET cc_start: 0.7239 (mmt) cc_final: 0.6661 (mmp) REVERT: A 756 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6520 (mt-10) REVERT: B 79 GLU cc_start: 0.7913 (tt0) cc_final: 0.6944 (mm-30) REVERT: B 170 ARG cc_start: 0.7886 (ttm170) cc_final: 0.6580 (pmt170) REVERT: B 222 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7540 (mtm-85) REVERT: B 238 LYS cc_start: 0.7267 (ttpp) cc_final: 0.6940 (ttmm) REVERT: B 257 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 331 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6986 (tm) REVERT: B 340 LEU cc_start: 0.7453 (mm) cc_final: 0.7250 (mt) REVERT: B 380 MET cc_start: 0.7582 (mtm) cc_final: 0.7193 (mmp) REVERT: B 382 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7441 (mp) REVERT: B 393 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5409 (mt) REVERT: B 422 MET cc_start: 0.7500 (tpp) cc_final: 0.6682 (ttp) REVERT: B 429 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: B 512 ARG cc_start: 0.7640 (tpt90) cc_final: 0.7240 (tpp80) REVERT: B 529 LEU cc_start: 0.8037 (tp) cc_final: 0.7767 (mt) REVERT: B 551 ASN cc_start: 0.8447 (t0) cc_final: 0.8053 (t0) REVERT: B 570 GLU cc_start: 0.8548 (tp30) cc_final: 0.8260 (mm-30) REVERT: B 728 MET cc_start: 0.7234 (mmt) cc_final: 0.6655 (mmp) REVERT: B 756 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6536 (mt-10) REVERT: C 79 GLU cc_start: 0.7958 (tt0) cc_final: 0.6915 (mm-30) REVERT: C 222 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7564 (mtm-85) REVERT: C 238 LYS cc_start: 0.7248 (ttpp) cc_final: 0.6918 (ttmm) REVERT: C 257 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: C 361 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7766 (tttt) REVERT: C 380 MET cc_start: 0.7590 (mtm) cc_final: 0.7204 (mmp) REVERT: C 382 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7453 (mp) REVERT: C 393 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5400 (mt) REVERT: C 422 MET cc_start: 0.7520 (tpp) cc_final: 0.6713 (ttp) REVERT: C 512 ARG cc_start: 0.7638 (tpt90) cc_final: 0.7231 (tpp80) REVERT: C 529 LEU cc_start: 0.8100 (tp) cc_final: 0.7808 (mt) REVERT: C 551 ASN cc_start: 0.8529 (t0) cc_final: 0.8184 (t0) REVERT: C 728 MET cc_start: 0.7324 (mmt) cc_final: 0.6903 (mmp) REVERT: C 756 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6543 (mt-10) REVERT: D 79 GLU cc_start: 0.7963 (tt0) cc_final: 0.6923 (mm-30) REVERT: D 167 THR cc_start: 0.8326 (p) cc_final: 0.8112 (m) REVERT: D 222 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7558 (mtm-85) REVERT: D 238 LYS cc_start: 0.7247 (ttpp) cc_final: 0.6920 (ttmm) REVERT: D 257 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: D 340 LEU cc_start: 0.7450 (mm) cc_final: 0.7236 (mt) REVERT: D 361 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7776 (tttt) REVERT: D 380 MET cc_start: 0.7664 (mtm) cc_final: 0.7272 (mmp) REVERT: D 382 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7445 (mp) REVERT: D 393 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5405 (mt) REVERT: D 422 MET cc_start: 0.7507 (tpp) cc_final: 0.6681 (ttp) REVERT: D 512 ARG cc_start: 0.7623 (tpt90) cc_final: 0.7222 (tpp80) REVERT: D 529 LEU cc_start: 0.8093 (tp) cc_final: 0.7801 (mt) REVERT: D 551 ASN cc_start: 0.8539 (t0) cc_final: 0.8190 (t0) REVERT: D 728 MET cc_start: 0.7235 (mmt) cc_final: 0.6656 (mmp) REVERT: D 756 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6514 (mt-10) outliers start: 54 outliers final: 10 residues processed: 349 average time/residue: 0.5397 time to fit residues: 217.9885 Evaluate side-chains 316 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 6.9990 chunk 97 optimal weight: 0.0670 chunk 257 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 533 ASN B 326 HIS B 533 ASN C 326 HIS C 533 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115990 restraints weight = 23678.269| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.17 r_work: 0.3243 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22996 Z= 0.104 Angle : 0.424 6.197 31072 Z= 0.217 Chirality : 0.034 0.151 3468 Planarity : 0.003 0.047 3812 Dihedral : 10.512 151.153 3308 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.31 % Allowed : 14.35 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.16), residues: 2628 helix: 2.57 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 191 TYR 0.012 0.001 TYR A 524 PHE 0.018 0.001 PHE D 341 TRP 0.014 0.001 TRP D 315 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (22976) covalent geometry : angle 0.42368 / 0.22 (31052) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.42281 / 0.29 ( 8) hydrogen bonds : bond 0.03734 / 2.49 ( 1484) hydrogen bonds : angle 3.52967 / 2.58 ( 4344) metal coordination : bond 0.00223 / 0.19 ( 16) metal coordination : angle 0.55506 / 0.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7901 (tt0) cc_final: 0.6970 (mm-30) REVERT: A 222 ARG cc_start: 0.7902 (ptp-170) cc_final: 0.7532 (mtm-85) REVERT: A 257 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: A 331 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7035 (tm) REVERT: A 361 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7698 (tttt) REVERT: A 380 MET cc_start: 0.7555 (mtm) cc_final: 0.7190 (mmp) REVERT: A 393 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5381 (mt) REVERT: A 422 MET cc_start: 0.7500 (tpp) cc_final: 0.6723 (ttp) REVERT: A 512 ARG cc_start: 0.7715 (tpt90) cc_final: 0.7289 (tpp80) REVERT: A 516 ASP cc_start: 0.6389 (m-30) cc_final: 0.6171 (m-30) REVERT: A 529 LEU cc_start: 0.8062 (tp) cc_final: 0.7789 (mt) REVERT: A 551 ASN cc_start: 0.8420 (t0) cc_final: 0.8078 (t0) REVERT: A 728 MET cc_start: 0.7252 (mmt) cc_final: 0.6814 (mmp) REVERT: A 756 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6533 (mt-10) REVERT: A 758 LEU cc_start: 0.6752 (mt) cc_final: 0.6462 (mt) REVERT: B 79 GLU cc_start: 0.7901 (tt0) cc_final: 0.6978 (mm-30) REVERT: B 170 ARG cc_start: 0.7879 (ttm170) cc_final: 0.6574 (pmt170) REVERT: B 222 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7541 (mtm-85) REVERT: B 257 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: B 331 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6972 (tm) REVERT: B 380 MET cc_start: 0.7548 (mtm) cc_final: 0.7215 (mmp) REVERT: B 382 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7421 (mp) REVERT: B 393 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5395 (mt) REVERT: B 422 MET cc_start: 0.7516 (tpp) cc_final: 0.6700 (ttp) REVERT: B 512 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7289 (tpp80) REVERT: B 529 LEU cc_start: 0.8072 (tp) cc_final: 0.7812 (mt) REVERT: B 551 ASN cc_start: 0.8417 (t0) cc_final: 0.8071 (t0) REVERT: B 570 GLU cc_start: 0.8520 (tp30) cc_final: 0.8226 (mm-30) REVERT: B 728 MET cc_start: 0.7251 (mmt) cc_final: 0.6814 (mmp) REVERT: B 756 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6520 (mt-10) REVERT: C 79 GLU cc_start: 0.7927 (tt0) cc_final: 0.6943 (mm-30) REVERT: C 222 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7543 (mtm-85) REVERT: C 331 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6936 (tm) REVERT: C 361 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7776 (tttt) REVERT: C 380 MET cc_start: 0.7552 (mtm) cc_final: 0.7222 (mmp) REVERT: C 382 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7445 (mp) REVERT: C 393 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5383 (mt) REVERT: C 422 MET cc_start: 0.7529 (tpp) cc_final: 0.6745 (ttp) REVERT: C 512 ARG cc_start: 0.7707 (tpt90) cc_final: 0.7300 (tpp80) REVERT: C 529 LEU cc_start: 0.8168 (tp) cc_final: 0.7887 (mt) REVERT: C 551 ASN cc_start: 0.8481 (t0) cc_final: 0.8067 (t0) REVERT: C 756 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6504 (mt-10) REVERT: C 758 LEU cc_start: 0.6825 (mt) cc_final: 0.6540 (mt) REVERT: D 79 GLU cc_start: 0.7938 (tt0) cc_final: 0.6945 (mm-30) REVERT: D 222 ARG cc_start: 0.7904 (ptp-170) cc_final: 0.7538 (mtm-85) REVERT: D 257 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: D 331 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6927 (tm) REVERT: D 361 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7787 (tttt) REVERT: D 380 MET cc_start: 0.7565 (mtm) cc_final: 0.7199 (mmp) REVERT: D 382 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7434 (mp) REVERT: D 393 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5381 (mt) REVERT: D 422 MET cc_start: 0.7525 (tpp) cc_final: 0.6739 (ttp) REVERT: D 512 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7281 (tpp80) REVERT: D 529 LEU cc_start: 0.8149 (tp) cc_final: 0.7867 (mt) REVERT: D 551 ASN cc_start: 0.8490 (t0) cc_final: 0.8077 (t0) REVERT: D 728 MET cc_start: 0.7217 (mmt) cc_final: 0.6780 (mmp) REVERT: D 756 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6517 (mt-10) REVERT: D 758 LEU cc_start: 0.6740 (mt) cc_final: 0.6434 (mt) outliers start: 55 outliers final: 13 residues processed: 332 average time/residue: 0.5546 time to fit residues: 214.1816 Evaluate side-chains 312 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 145 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 533 ASN B 326 HIS B 533 ASN C 326 HIS C 533 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115230 restraints weight = 23931.890| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.19 r_work: 0.3235 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22996 Z= 0.119 Angle : 0.439 6.166 31072 Z= 0.223 Chirality : 0.035 0.151 3468 Planarity : 0.004 0.047 3812 Dihedral : 10.193 149.774 3308 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.89 % Allowed : 15.65 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.16), residues: 2628 helix: 2.56 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : 0.00 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.014 0.001 TYR A 524 PHE 0.018 0.001 PHE A 341 TRP 0.013 0.001 TRP D 315 HIS 0.002 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22976) covalent geometry : angle 0.43867 / 0.22 (31052) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 0.41645 / 0.29 ( 8) hydrogen bonds : bond 0.03875 / 2.59 ( 1484) hydrogen bonds : angle 3.53958 / 2.59 ( 4344) metal coordination : bond 0.00258 / 0.22 ( 16) metal coordination : angle 0.42151 / 0.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 0.887 Fit side-chains REVERT: A 79 GLU cc_start: 0.7904 (tt0) cc_final: 0.6938 (mm-30) REVERT: A 81 GLU cc_start: 0.6571 (mt-10) cc_final: 0.5873 (tm-30) REVERT: A 170 ARG cc_start: 0.7855 (ttm170) cc_final: 0.6574 (pmt170) REVERT: A 222 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7526 (mtm-85) REVERT: A 257 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: A 331 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6944 (tm) REVERT: A 361 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7701 (tttt) REVERT: A 380 MET cc_start: 0.7564 (mtm) cc_final: 0.7242 (mmp) REVERT: A 393 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5378 (mt) REVERT: A 422 MET cc_start: 0.7515 (tpp) cc_final: 0.6695 (ttp) REVERT: A 512 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7295 (tpp80) REVERT: A 529 LEU cc_start: 0.8082 (tp) cc_final: 0.7813 (mt) REVERT: A 551 ASN cc_start: 0.8433 (t0) cc_final: 0.8128 (t0) REVERT: A 728 MET cc_start: 0.7253 (mmt) cc_final: 0.6618 (mmp) REVERT: A 756 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 758 LEU cc_start: 0.6690 (mt) cc_final: 0.6407 (mt) REVERT: B 79 GLU cc_start: 0.7916 (tt0) cc_final: 0.6955 (mm-30) REVERT: B 81 GLU cc_start: 0.6529 (mt-10) cc_final: 0.5846 (tm-30) REVERT: B 170 ARG cc_start: 0.7856 (ttm170) cc_final: 0.6587 (pmt170) REVERT: B 222 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7524 (mtm-85) REVERT: B 257 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: B 331 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6957 (tm) REVERT: B 380 MET cc_start: 0.7574 (mtm) cc_final: 0.7250 (mmp) REVERT: B 393 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5379 (mt) REVERT: B 422 MET cc_start: 0.7519 (tpp) cc_final: 0.6696 (ttp) REVERT: B 512 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7275 (tpp80) REVERT: B 529 LEU cc_start: 0.8033 (tp) cc_final: 0.7779 (mt) REVERT: B 551 ASN cc_start: 0.8424 (t0) cc_final: 0.8117 (t0) REVERT: B 570 GLU cc_start: 0.8508 (tp30) cc_final: 0.8207 (mm-30) REVERT: B 728 MET cc_start: 0.7205 (mmt) cc_final: 0.6559 (mmp) REVERT: B 756 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6664 (mt-10) REVERT: B 758 LEU cc_start: 0.6710 (mt) cc_final: 0.6427 (mt) REVERT: C 79 GLU cc_start: 0.7926 (tt0) cc_final: 0.6939 (mm-30) REVERT: C 81 GLU cc_start: 0.6587 (mt-10) cc_final: 0.5886 (tm-30) REVERT: C 170 ARG cc_start: 0.7847 (ttm170) cc_final: 0.6574 (pmt170) REVERT: C 222 ARG cc_start: 0.7881 (ptp-170) cc_final: 0.7529 (mtm-85) REVERT: C 331 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6922 (tm) REVERT: C 361 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7770 (tttt) REVERT: C 380 MET cc_start: 0.7563 (mtm) cc_final: 0.7242 (mmp) REVERT: C 393 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5368 (mt) REVERT: C 422 MET cc_start: 0.7498 (tpp) cc_final: 0.6691 (ttp) REVERT: C 512 ARG cc_start: 0.7763 (tpt90) cc_final: 0.7281 (tpp80) REVERT: C 529 LEU cc_start: 0.8089 (tp) cc_final: 0.7817 (mt) REVERT: C 551 ASN cc_start: 0.8444 (t0) cc_final: 0.8124 (t0) REVERT: C 728 MET cc_start: 0.7196 (mmt) cc_final: 0.6650 (mmp) REVERT: C 756 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6648 (mt-10) REVERT: C 758 LEU cc_start: 0.6663 (mt) cc_final: 0.6374 (mt) REVERT: D 79 GLU cc_start: 0.7931 (tt0) cc_final: 0.6954 (mm-30) REVERT: D 81 GLU cc_start: 0.6598 (mt-10) cc_final: 0.5889 (tm-30) REVERT: D 170 ARG cc_start: 0.7854 (ttm170) cc_final: 0.6578 (pmt170) REVERT: D 222 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7534 (mtm-85) REVERT: D 257 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: D 331 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6925 (tm) REVERT: D 380 MET cc_start: 0.7569 (mtm) cc_final: 0.7247 (mmp) REVERT: D 393 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5349 (mt) REVERT: D 422 MET cc_start: 0.7491 (tpp) cc_final: 0.6678 (ttp) REVERT: D 512 ARG cc_start: 0.7739 (tpt90) cc_final: 0.7263 (tpp80) REVERT: D 529 LEU cc_start: 0.8085 (tp) cc_final: 0.7811 (mt) REVERT: D 551 ASN cc_start: 0.8453 (t0) cc_final: 0.8056 (t0) REVERT: D 728 MET cc_start: 0.7250 (mmt) cc_final: 0.6802 (mmp) REVERT: D 756 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6677 (mt-10) REVERT: D 758 LEU cc_start: 0.6695 (mt) cc_final: 0.6398 (mt) outliers start: 45 outliers final: 18 residues processed: 326 average time/residue: 0.5796 time to fit residues: 219.5129 Evaluate side-chains 310 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 533 ASN B 326 HIS B 533 ASN C 326 HIS C 533 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112983 restraints weight = 23979.019| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.18 r_work: 0.3204 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22996 Z= 0.172 Angle : 0.481 6.282 31072 Z= 0.244 Chirality : 0.036 0.165 3468 Planarity : 0.004 0.047 3812 Dihedral : 10.439 149.082 3308 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.47 % Allowed : 14.93 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.16), residues: 2628 helix: 2.36 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.17 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 557 TYR 0.018 0.001 TYR A 524 PHE 0.019 0.002 PHE A 520 TRP 0.013 0.001 TRP B 315 HIS 0.002 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (22976) covalent geometry : angle 0.48133 / 0.24 (31052) SS BOND : bond 0.00150 / 0.08 ( 4) SS BOND : angle 0.49783 / 0.33 ( 8) hydrogen bonds : bond 0.04362 / 2.92 ( 1484) hydrogen bonds : angle 3.63790 / 2.66 ( 4344) metal coordination : bond 0.00405 / 0.37 ( 16) metal coordination : angle 0.46474 / 0.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 292 time to evaluate : 0.897 Fit side-chains REVERT: A 79 GLU cc_start: 0.7948 (tt0) cc_final: 0.7014 (mm-30) REVERT: A 81 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6100 (tm-30) REVERT: A 222 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7604 (mtm-85) REVERT: A 238 LYS cc_start: 0.7456 (ttpp) cc_final: 0.7123 (ttmm) REVERT: A 257 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: A 331 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6977 (tm) REVERT: A 361 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7753 (tttt) REVERT: A 380 MET cc_start: 0.7619 (mtm) cc_final: 0.7303 (mmp) REVERT: A 393 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5294 (mt) REVERT: A 422 MET cc_start: 0.7516 (tpp) cc_final: 0.6777 (ttp) REVERT: A 512 ARG cc_start: 0.7844 (tpt90) cc_final: 0.7291 (tpp80) REVERT: A 529 LEU cc_start: 0.8188 (tp) cc_final: 0.7923 (mt) REVERT: A 551 ASN cc_start: 0.8475 (t0) cc_final: 0.8151 (t0) REVERT: A 728 MET cc_start: 0.7318 (mmt) cc_final: 0.6849 (mmp) REVERT: A 756 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 79 GLU cc_start: 0.7959 (tt0) cc_final: 0.7024 (mm-30) REVERT: B 81 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6113 (tm-30) REVERT: B 222 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7595 (mtm-85) REVERT: B 238 LYS cc_start: 0.7473 (ttpp) cc_final: 0.7142 (ttmm) REVERT: B 257 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: B 331 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6978 (tm) REVERT: B 380 MET cc_start: 0.7611 (mtm) cc_final: 0.7302 (mmp) REVERT: B 393 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5307 (mt) REVERT: B 422 MET cc_start: 0.7553 (tpp) cc_final: 0.6794 (ttp) REVERT: B 512 ARG cc_start: 0.7846 (tpt90) cc_final: 0.7286 (tpp80) REVERT: B 529 LEU cc_start: 0.8130 (tp) cc_final: 0.7885 (mt) REVERT: B 551 ASN cc_start: 0.8466 (t0) cc_final: 0.8139 (t0) REVERT: B 570 GLU cc_start: 0.8568 (tp30) cc_final: 0.8266 (mm-30) REVERT: B 728 MET cc_start: 0.7315 (mmt) cc_final: 0.6846 (mmp) REVERT: B 756 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6797 (mt-10) REVERT: C 79 GLU cc_start: 0.7966 (tt0) cc_final: 0.7005 (mm-30) REVERT: C 81 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6114 (tm-30) REVERT: C 222 ARG cc_start: 0.7983 (ptp-170) cc_final: 0.7605 (mtm-85) REVERT: C 238 LYS cc_start: 0.7457 (ttpp) cc_final: 0.7123 (ttmm) REVERT: C 331 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6965 (tm) REVERT: C 361 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7809 (tttt) REVERT: C 380 MET cc_start: 0.7616 (mtm) cc_final: 0.7303 (mmp) REVERT: C 393 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5392 (mt) REVERT: C 422 MET cc_start: 0.7548 (tpp) cc_final: 0.6791 (ttp) REVERT: C 512 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7297 (tpp80) REVERT: C 529 LEU cc_start: 0.8193 (tp) cc_final: 0.7927 (mt) REVERT: C 551 ASN cc_start: 0.8548 (t0) cc_final: 0.8204 (t0) REVERT: C 728 MET cc_start: 0.7313 (mmt) cc_final: 0.6862 (mmp) REVERT: C 756 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6808 (mt-10) REVERT: D 79 GLU cc_start: 0.7976 (tt0) cc_final: 0.7005 (mm-30) REVERT: D 81 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6145 (tm-30) REVERT: D 222 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7605 (mtm-85) REVERT: D 238 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7224 (ttmm) REVERT: D 257 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: D 331 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6977 (tm) REVERT: D 380 MET cc_start: 0.7615 (mtm) cc_final: 0.7299 (mmp) REVERT: D 393 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5297 (mt) REVERT: D 422 MET cc_start: 0.7537 (tpp) cc_final: 0.6784 (ttp) REVERT: D 512 ARG cc_start: 0.7836 (tpt90) cc_final: 0.7284 (tpp80) REVERT: D 529 LEU cc_start: 0.8191 (tp) cc_final: 0.7925 (mt) REVERT: D 551 ASN cc_start: 0.8555 (t0) cc_final: 0.8211 (t0) REVERT: D 728 MET cc_start: 0.7304 (mmt) cc_final: 0.6828 (mmp) REVERT: D 756 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6810 (mt-10) REVERT: D 758 LEU cc_start: 0.6730 (mt) cc_final: 0.6440 (mt) outliers start: 59 outliers final: 23 residues processed: 328 average time/residue: 0.6050 time to fit residues: 229.1011 Evaluate side-chains 321 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 285 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 67 optimal weight: 0.0030 chunk 250 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 326 HIS A 533 ASN B 326 HIS B 533 ASN C 326 HIS C 533 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115527 restraints weight = 23745.823| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.18 r_work: 0.3242 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22996 Z= 0.106 Angle : 0.439 6.654 31072 Z= 0.224 Chirality : 0.034 0.161 3468 Planarity : 0.003 0.048 3812 Dihedral : 10.032 146.950 3308 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.68 % Allowed : 16.65 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.16), residues: 2628 helix: 2.56 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.10 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.011 0.001 TYR A 524 PHE 0.016 0.001 PHE B 341 TRP 0.015 0.001 TRP C 315 HIS 0.002 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (22976) covalent geometry : angle 0.43859 / 0.22 (31052) SS BOND : bond 0.00062 / 0.03 ( 4) SS BOND : angle 0.27790 / 0.20 ( 8) hydrogen bonds : bond 0.03770 / 2.52 ( 1484) hydrogen bonds : angle 3.54919 / 2.59 ( 4344) metal coordination : bond 0.00253 / 0.23 ( 16) metal coordination : angle 0.49605 / 0.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.640 Fit side-chains REVERT: A 79 GLU cc_start: 0.7905 (tt0) cc_final: 0.6951 (mm-30) REVERT: A 81 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6087 (tm-30) REVERT: A 170 ARG cc_start: 0.7859 (ttm170) cc_final: 0.6553 (pmt170) REVERT: A 222 ARG cc_start: 0.7835 (ptp-170) cc_final: 0.7483 (mtm-85) REVERT: A 257 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 331 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6937 (tm) REVERT: A 361 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7687 (tttt) REVERT: A 380 MET cc_start: 0.7520 (mtm) cc_final: 0.7254 (mmp) REVERT: A 393 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5304 (mt) REVERT: A 422 MET cc_start: 0.7511 (tpp) cc_final: 0.6891 (ttp) REVERT: A 512 ARG cc_start: 0.7802 (tpt90) cc_final: 0.7253 (tpp80) REVERT: A 529 LEU cc_start: 0.8090 (tp) cc_final: 0.7839 (mt) REVERT: A 551 ASN cc_start: 0.8405 (t0) cc_final: 0.8061 (t0) REVERT: A 728 MET cc_start: 0.7235 (mmt) cc_final: 0.6600 (mmp) REVERT: A 756 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6724 (mt-10) REVERT: A 758 LEU cc_start: 0.6705 (mt) cc_final: 0.6412 (mt) REVERT: B 79 GLU cc_start: 0.7920 (tt0) cc_final: 0.6973 (mm-30) REVERT: B 81 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6049 (tm-30) REVERT: B 170 ARG cc_start: 0.7835 (ttm170) cc_final: 0.6548 (pmt170) REVERT: B 222 ARG cc_start: 0.7833 (ptp-170) cc_final: 0.7485 (mtm-85) REVERT: B 257 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 331 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6950 (tm) REVERT: B 380 MET cc_start: 0.7515 (mtm) cc_final: 0.7250 (mmp) REVERT: B 393 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5326 (mt) REVERT: B 422 MET cc_start: 0.7492 (tpp) cc_final: 0.6801 (ttp) REVERT: B 512 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7254 (tpp80) REVERT: B 529 LEU cc_start: 0.8100 (tp) cc_final: 0.7854 (mt) REVERT: B 551 ASN cc_start: 0.8402 (t0) cc_final: 0.8056 (t0) REVERT: B 570 GLU cc_start: 0.8483 (tp30) cc_final: 0.8181 (mm-30) REVERT: B 728 MET cc_start: 0.7224 (mmt) cc_final: 0.6589 (mmp) REVERT: B 756 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6723 (mt-10) REVERT: B 758 LEU cc_start: 0.6658 (mt) cc_final: 0.6384 (mt) REVERT: C 79 GLU cc_start: 0.7916 (tt0) cc_final: 0.6971 (mm-30) REVERT: C 81 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6098 (tm-30) REVERT: C 170 ARG cc_start: 0.7796 (ttm170) cc_final: 0.6490 (pmt170) REVERT: C 222 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7495 (mtm-85) REVERT: C 331 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6939 (tm) REVERT: C 380 MET cc_start: 0.7500 (mtm) cc_final: 0.7236 (mmp) REVERT: C 393 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5296 (mt) REVERT: C 422 MET cc_start: 0.7553 (tpp) cc_final: 0.6879 (ttp) REVERT: C 512 ARG cc_start: 0.7833 (tpt90) cc_final: 0.7260 (tpp80) REVERT: C 529 LEU cc_start: 0.8093 (tp) cc_final: 0.7839 (mt) REVERT: C 551 ASN cc_start: 0.8414 (t0) cc_final: 0.8077 (t0) REVERT: C 728 MET cc_start: 0.7232 (mmt) cc_final: 0.6783 (mmp) REVERT: C 756 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6707 (mt-10) REVERT: C 758 LEU cc_start: 0.6675 (mt) cc_final: 0.6408 (mt) REVERT: D 79 GLU cc_start: 0.7902 (tt0) cc_final: 0.6959 (mm-30) REVERT: D 81 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6066 (tm-30) REVERT: D 170 ARG cc_start: 0.7859 (ttm170) cc_final: 0.6558 (pmt170) REVERT: D 222 ARG cc_start: 0.7855 (ptp-170) cc_final: 0.7507 (mtm-85) REVERT: D 257 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: D 331 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6927 (tm) REVERT: D 380 MET cc_start: 0.7515 (mtm) cc_final: 0.7248 (mmp) REVERT: D 393 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5307 (mt) REVERT: D 422 MET cc_start: 0.7522 (tpp) cc_final: 0.6907 (ttp) REVERT: D 512 ARG cc_start: 0.7820 (tpt90) cc_final: 0.7240 (tpp80) REVERT: D 529 LEU cc_start: 0.8092 (tp) cc_final: 0.7834 (mt) REVERT: D 551 ASN cc_start: 0.8506 (t0) cc_final: 0.8162 (t0) REVERT: D 728 MET cc_start: 0.7217 (mmt) cc_final: 0.6581 (mmp) REVERT: D 756 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6717 (mt-10) REVERT: D 758 LEU cc_start: 0.6728 (mt) cc_final: 0.6449 (mt) outliers start: 40 outliers final: 18 residues processed: 322 average time/residue: 0.5741 time to fit residues: 214.8052 Evaluate side-chains 311 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 43 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 0.0050 chunk 122 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 533 ASN B 326 HIS B 533 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS C 533 ASN C 711 GLN C 742 ASN D 326 HIS D 533 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116765 restraints weight = 23899.467| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.19 r_work: 0.3250 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22996 Z= 0.099 Angle : 0.427 6.200 31072 Z= 0.218 Chirality : 0.034 0.152 3468 Planarity : 0.003 0.049 3812 Dihedral : 9.745 142.775 3308 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.47 % Allowed : 17.07 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.16), residues: 2628 helix: 2.62 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.09 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.012 0.001 TYR A 524 PHE 0.025 0.001 PHE A 520 TRP 0.016 0.001 TRP C 315 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22976) covalent geometry : angle 0.42702 / 0.22 (31052) SS BOND : bond 0.00052 / 0.03 ( 4) SS BOND : angle 0.29383 / 0.21 ( 8) hydrogen bonds : bond 0.03583 / 2.40 ( 1484) hydrogen bonds : angle 3.49046 / 2.55 ( 4344) metal coordination : bond 0.00231 / 0.21 ( 16) metal coordination : angle 0.46923 / 0.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.686 Fit side-chains REVERT: A 79 GLU cc_start: 0.7905 (tt0) cc_final: 0.6961 (mm-30) REVERT: A 81 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6089 (tm-30) REVERT: A 170 ARG cc_start: 0.7825 (ttm170) cc_final: 0.6480 (pmt170) REVERT: A 222 ARG cc_start: 0.7830 (ptp-170) cc_final: 0.7480 (mtm-85) REVERT: A 257 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: A 331 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6836 (tm) REVERT: A 361 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7770 (tttt) REVERT: A 380 MET cc_start: 0.7509 (mtm) cc_final: 0.7264 (mmp) REVERT: A 393 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5273 (mt) REVERT: A 422 MET cc_start: 0.7510 (tpp) cc_final: 0.6911 (ttp) REVERT: A 512 ARG cc_start: 0.7839 (tpt90) cc_final: 0.7268 (tpp80) REVERT: A 529 LEU cc_start: 0.8095 (tp) cc_final: 0.7848 (mt) REVERT: A 551 ASN cc_start: 0.8382 (t0) cc_final: 0.8052 (t0) REVERT: A 728 MET cc_start: 0.7231 (mmt) cc_final: 0.6754 (mmp) REVERT: A 756 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6757 (mt-10) REVERT: A 758 LEU cc_start: 0.6668 (mt) cc_final: 0.6392 (mt) REVERT: B 79 GLU cc_start: 0.7934 (tt0) cc_final: 0.6991 (mm-30) REVERT: B 81 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6041 (tm-30) REVERT: B 170 ARG cc_start: 0.7811 (ttm170) cc_final: 0.6474 (pmt170) REVERT: B 222 ARG cc_start: 0.7824 (ptp-170) cc_final: 0.7475 (mtm-85) REVERT: B 257 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 331 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6829 (tm) REVERT: B 380 MET cc_start: 0.7511 (mtm) cc_final: 0.7266 (mmp) REVERT: B 393 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5298 (mt) REVERT: B 422 MET cc_start: 0.7464 (tpp) cc_final: 0.6834 (ttp) REVERT: B 512 ARG cc_start: 0.7840 (tpt90) cc_final: 0.7273 (tpp80) REVERT: B 529 LEU cc_start: 0.8092 (tp) cc_final: 0.7852 (mt) REVERT: B 551 ASN cc_start: 0.8376 (t0) cc_final: 0.8045 (t0) REVERT: B 570 GLU cc_start: 0.8467 (tp30) cc_final: 0.8179 (mm-30) REVERT: B 728 MET cc_start: 0.7217 (mmt) cc_final: 0.6738 (mmp) REVERT: B 756 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6731 (mt-10) REVERT: B 758 LEU cc_start: 0.6723 (mt) cc_final: 0.6482 (mt) REVERT: C 79 GLU cc_start: 0.7938 (tt0) cc_final: 0.6999 (mm-30) REVERT: C 81 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6038 (tm-30) REVERT: C 170 ARG cc_start: 0.7810 (ttm170) cc_final: 0.6468 (pmt170) REVERT: C 222 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7497 (mtm-85) REVERT: C 331 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6847 (tm) REVERT: C 380 MET cc_start: 0.7495 (mtm) cc_final: 0.7256 (mmp) REVERT: C 393 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5298 (mt) REVERT: C 422 MET cc_start: 0.7529 (tpp) cc_final: 0.6936 (ttp) REVERT: C 512 ARG cc_start: 0.7853 (tpt90) cc_final: 0.7289 (tpp80) REVERT: C 529 LEU cc_start: 0.8093 (tp) cc_final: 0.7848 (mt) REVERT: C 551 ASN cc_start: 0.8376 (t0) cc_final: 0.7997 (t0) REVERT: C 728 MET cc_start: 0.7219 (mmt) cc_final: 0.6740 (mmp) REVERT: C 756 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6712 (mt-10) REVERT: C 758 LEU cc_start: 0.6671 (mt) cc_final: 0.6399 (mt) REVERT: D 79 GLU cc_start: 0.7927 (tt0) cc_final: 0.6985 (mm-30) REVERT: D 81 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6099 (tm-30) REVERT: D 170 ARG cc_start: 0.7819 (ttm170) cc_final: 0.6480 (pmt170) REVERT: D 222 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.7511 (mtm-85) REVERT: D 331 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6846 (tm) REVERT: D 380 MET cc_start: 0.7509 (mtm) cc_final: 0.7265 (mmp) REVERT: D 393 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5269 (mt) REVERT: D 422 MET cc_start: 0.7521 (tpp) cc_final: 0.6828 (ttp) REVERT: D 512 ARG cc_start: 0.7821 (tpt90) cc_final: 0.7268 (tpp80) REVERT: D 529 LEU cc_start: 0.8097 (tp) cc_final: 0.7846 (mt) REVERT: D 551 ASN cc_start: 0.8388 (t0) cc_final: 0.8012 (t0) REVERT: D 728 MET cc_start: 0.7211 (mmt) cc_final: 0.6732 (mmp) REVERT: D 756 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6728 (mt-10) REVERT: D 758 LEU cc_start: 0.6672 (mt) cc_final: 0.6409 (mt) outliers start: 35 outliers final: 17 residues processed: 305 average time/residue: 0.5447 time to fit residues: 193.1067 Evaluate side-chains 303 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 77 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 533 ASN A 711 GLN B 326 HIS B 533 ASN B 711 GLN C 326 HIS C 533 ASN C 711 GLN D 326 HIS D 533 ASN D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115591 restraints weight = 23970.370| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.20 r_work: 0.3237 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22996 Z= 0.113 Angle : 0.449 7.059 31072 Z= 0.226 Chirality : 0.034 0.151 3468 Planarity : 0.003 0.047 3812 Dihedral : 9.815 141.953 3308 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.34 % Allowed : 16.95 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.16), residues: 2628 helix: 2.58 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.13 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 191 TYR 0.013 0.001 TYR C 524 PHE 0.017 0.001 PHE B 341 TRP 0.013 0.001 TRP D 315 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (22976) covalent geometry : angle 0.44860 / 0.23 (31052) SS BOND : bond 0.00069 / 0.03 ( 4) SS BOND : angle 0.30141 / 0.21 ( 8) hydrogen bonds : bond 0.03761 / 2.52 ( 1484) hydrogen bonds : angle 3.49496 / 2.55 ( 4344) metal coordination : bond 0.00279 / 0.25 ( 16) metal coordination : angle 0.47846 / 0.30 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.827 Fit side-chains REVERT: A 79 GLU cc_start: 0.7911 (tt0) cc_final: 0.6962 (mm-30) REVERT: A 81 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6073 (tm-30) REVERT: A 170 ARG cc_start: 0.7849 (ttm170) cc_final: 0.6474 (pmt170) REVERT: A 222 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7506 (mtm-85) REVERT: A 257 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: A 331 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6861 (tm) REVERT: A 361 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7779 (tttt) REVERT: A 380 MET cc_start: 0.7517 (mtm) cc_final: 0.7261 (mmp) REVERT: A 393 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5357 (mt) REVERT: A 422 MET cc_start: 0.7512 (tpp) cc_final: 0.6910 (ttp) REVERT: A 512 ARG cc_start: 0.7875 (tpt90) cc_final: 0.7295 (tpp80) REVERT: A 529 LEU cc_start: 0.8109 (tp) cc_final: 0.7857 (mt) REVERT: A 551 ASN cc_start: 0.8395 (t0) cc_final: 0.8030 (t0) REVERT: A 728 MET cc_start: 0.7242 (mmt) cc_final: 0.6758 (mmp) REVERT: A 756 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 758 LEU cc_start: 0.6651 (mt) cc_final: 0.6393 (mt) REVERT: B 79 GLU cc_start: 0.7939 (tt0) cc_final: 0.7001 (mm-30) REVERT: B 81 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6097 (tm-30) REVERT: B 170 ARG cc_start: 0.7786 (ttm170) cc_final: 0.6459 (pmt170) REVERT: B 222 ARG cc_start: 0.7865 (ptp-170) cc_final: 0.7512 (mtm-85) REVERT: B 257 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: B 331 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6856 (tm) REVERT: B 380 MET cc_start: 0.7514 (mtm) cc_final: 0.7264 (mmp) REVERT: B 393 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5391 (mt) REVERT: B 422 MET cc_start: 0.7457 (tpp) cc_final: 0.6818 (ttp) REVERT: B 512 ARG cc_start: 0.7853 (tpt90) cc_final: 0.7252 (tpp80) REVERT: B 529 LEU cc_start: 0.8097 (tp) cc_final: 0.7855 (mt) REVERT: B 551 ASN cc_start: 0.8394 (t0) cc_final: 0.8057 (t0) REVERT: B 570 GLU cc_start: 0.8475 (tp30) cc_final: 0.8186 (mm-30) REVERT: B 728 MET cc_start: 0.7221 (mmt) cc_final: 0.6737 (mmp) REVERT: B 756 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6724 (mt-10) REVERT: B 758 LEU cc_start: 0.6664 (mt) cc_final: 0.6405 (mt) REVERT: C 79 GLU cc_start: 0.7923 (tt0) cc_final: 0.6984 (mm-30) REVERT: C 81 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6082 (tm-30) REVERT: C 170 ARG cc_start: 0.7829 (ttm170) cc_final: 0.6465 (pmt170) REVERT: C 222 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7524 (mtm-85) REVERT: C 331 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6839 (tm) REVERT: C 380 MET cc_start: 0.7506 (mtm) cc_final: 0.7256 (mmp) REVERT: C 393 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5379 (mt) REVERT: C 422 MET cc_start: 0.7509 (tpp) cc_final: 0.6924 (ttp) REVERT: C 512 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7259 (tpp80) REVERT: C 529 LEU cc_start: 0.8107 (tp) cc_final: 0.7857 (mt) REVERT: C 551 ASN cc_start: 0.8397 (t0) cc_final: 0.8015 (t0) REVERT: C 728 MET cc_start: 0.7231 (mmt) cc_final: 0.6742 (mmp) REVERT: C 756 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6717 (mt-10) REVERT: C 758 LEU cc_start: 0.6671 (mt) cc_final: 0.6420 (mt) REVERT: D 79 GLU cc_start: 0.7909 (tt0) cc_final: 0.6967 (mm-30) REVERT: D 81 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6072 (tm-30) REVERT: D 170 ARG cc_start: 0.7846 (ttm170) cc_final: 0.6478 (pmt170) REVERT: D 222 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7519 (mtm-85) REVERT: D 331 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6871 (tm) REVERT: D 380 MET cc_start: 0.7517 (mtm) cc_final: 0.7263 (mmp) REVERT: D 393 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5377 (mt) REVERT: D 422 MET cc_start: 0.7505 (tpp) cc_final: 0.6919 (ttp) REVERT: D 512 ARG cc_start: 0.7838 (tpt90) cc_final: 0.7247 (tpp80) REVERT: D 529 LEU cc_start: 0.8108 (tp) cc_final: 0.7859 (mt) REVERT: D 551 ASN cc_start: 0.8412 (t0) cc_final: 0.8034 (t0) REVERT: D 728 MET cc_start: 0.7229 (mmt) cc_final: 0.6743 (mmp) REVERT: D 756 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6725 (mt-10) REVERT: D 758 LEU cc_start: 0.6657 (mt) cc_final: 0.6413 (mt) outliers start: 32 outliers final: 19 residues processed: 303 average time/residue: 0.5255 time to fit residues: 184.9314 Evaluate side-chains 306 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 207 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 263 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 533 ASN A 711 GLN A 742 ASN B 326 HIS B 533 ASN B 711 GLN B 742 ASN C 326 HIS C 533 ASN C 711 GLN D 326 HIS D 533 ASN D 711 GLN D 742 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116667 restraints weight = 23826.886| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.19 r_work: 0.3249 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22996 Z= 0.102 Angle : 0.437 7.603 31072 Z= 0.219 Chirality : 0.034 0.152 3468 Planarity : 0.003 0.048 3812 Dihedral : 9.698 139.916 3308 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.34 % Allowed : 17.16 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.16), residues: 2628 helix: 2.62 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.08 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.012 0.001 TYR A 524 PHE 0.022 0.001 PHE C 520 TRP 0.015 0.001 TRP C 315 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (22976) covalent geometry : angle 0.43693 / 0.22 (31052) SS BOND : bond 0.00057 / 0.03 ( 4) SS BOND : angle 0.27681 / 0.20 ( 8) hydrogen bonds : bond 0.03584 / 2.40 ( 1484) hydrogen bonds : angle 3.47909 / 2.54 ( 4344) metal coordination : bond 0.00256 / 0.23 ( 16) metal coordination : angle 0.49042 / 0.29 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8025.13 seconds wall clock time: 137 minutes 25.01 seconds (8245.01 seconds total)