Starting phenix.real_space_refine on Sun Aug 24 22:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d4p_30575/08_2025/7d4p_30575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d4p_30575/08_2025/7d4p_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_30575/08_2025/7d4p_30575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d4p_30575/08_2025/7d4p_30575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d4p_30575/08_2025/7d4p_30575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d4p_30575/08_2025/7d4p_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-2.0-5787/lib/python3.9/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: 6.07, 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: 2.07 Conformation dependent library (CDL) restraints added in 999.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.71 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: 4.22 Time building geometry restraints manager: 2.66 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: 13696 32.83 - 65.67: 268 65.67 - 98.50: 44 98.50 - 131.34: 4 131.34 - 164.17: 8 Dihedral angle restraints: 14020 sinusoidal: 6104 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 14017 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: 0.06 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: 2.010 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.870 Find NCS groups from input model: 0.200 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 13.898 164.170 8856 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 aren 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 covalent geometry : bond 0.00698 (22976) covalent geometry : angle 0.79763 (31052) SS BOND : bond 0.00508 ( 4) SS BOND : angle 0.76098 ( 8) hydrogen bonds : bond 0.10950 ( 1484) hydrogen bonds : angle 5.06670 ( 4344) metal coordination : bond 0.01136 ( 16) metal coordination : angle 1.33825 ( 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 : 0.967 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: 0.7362 (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: 0.6713 (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: 0.7344 (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: 0.7072 (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: 0.7351 (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: 0.6591 (m-30) cc_final: 0.6352 (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: 0.6383 (mt-10) REVERT: D 222 ARG cc_start: 0.7814 (ptp-170) cc_final: 0.7300 (mtm-85) REVERT: D 238 LYS cc_start: 0.7304 (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: 0.7262 (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: 0.6774 time to fit residues: 390.0329 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 : 0.890 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 711 GLN B 247 GLN B 711 GLN C 247 GLN C 573 GLN C 711 GLN D 247 GLN D 533 ASN D 711 GLN 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 = 0.161688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116685 restraints weight = 23978.430| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.20 r_work: 0.3255 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22996 Z= 0.111 Angle : 0.479 7.265 31072 Z= 0.239 Chirality : 0.035 0.149 3468 Planarity : 0.003 0.038 3812 Dihedral : 13.268 171.130 3618 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.72 % Allowed : 12.96 % Favored : 85.32 % 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 aren not related in a simple way. whole: 2.94 (0.16), residues: 2628 helix: 2.48 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.32 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.015 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 covalent geometry : bond 0.00239 (22976) covalent geometry : angle 0.47849 (31052) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.58855 ( 8) hydrogen bonds : bond 0.04010 ( 1484) hydrogen bonds : angle 3.76621 ( 4344) metal coordination : bond 0.00494 ( 16) metal coordination : angle 1.43886 ( 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 365 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7983 (mmm) cc_final: 0.7670 (mmm) REVERT: A 79 GLU cc_start: 0.8087 (tt0) cc_final: 0.7062 (mm-30) REVERT: A 222 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7345 (mtm-85) REVERT: A 238 LYS cc_start: 0.7155 (ttpp) cc_final: 0.6812 (ttmm) REVERT: A 257 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 340 LEU cc_start: 0.7395 (mt) cc_final: 0.7066 (tp) REVERT: A 343 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7165 (ttm) REVERT: A 380 MET cc_start: 0.7305 (mtm) cc_final: 0.7021 (mmp) REVERT: A 393 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5382 (mt) REVERT: A 512 ARG cc_start: 0.7343 (tpt90) cc_final: 0.7126 (tpp80) REVERT: A 516 ASP cc_start: 0.6646 (m-30) cc_final: 0.6437 (m-30) REVERT: A 551 ASN cc_start: 0.8400 (t0) cc_final: 0.8082 (t0) REVERT: A 744 LYS cc_start: 0.7251 (tptt) cc_final: 0.6949 (tptp) REVERT: A 756 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6405 (mt-10) REVERT: A 760 LEU cc_start: 0.7743 (mp) cc_final: 0.7381 (mp) REVERT: B 66 MET cc_start: 0.7967 (mmm) cc_final: 0.7648 (mmm) REVERT: B 79 GLU cc_start: 0.8052 (tt0) cc_final: 0.7045 (mm-30) REVERT: B 222 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7345 (mtm-85) REVERT: B 238 LYS cc_start: 0.7160 (ttpp) cc_final: 0.6817 (ttmm) REVERT: B 257 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: B 340 LEU cc_start: 0.7374 (mt) cc_final: 0.7042 (tp) REVERT: B 343 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7153 (ttm) REVERT: B 380 MET cc_start: 0.7306 (mtm) cc_final: 0.7025 (mmp) REVERT: B 393 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5427 (mt) REVERT: B 512 ARG cc_start: 0.7362 (tpt90) cc_final: 0.7130 (tpp80) REVERT: B 551 ASN cc_start: 0.8398 (t0) cc_final: 0.8044 (t0) REVERT: B 570 GLU cc_start: 0.8523 (tp30) cc_final: 0.8197 (mm-30) REVERT: B 744 LYS cc_start: 0.7261 (tptt) cc_final: 0.6966 (tptp) REVERT: B 756 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6408 (mt-10) REVERT: B 760 LEU cc_start: 0.7769 (mp) cc_final: 0.7411 (mp) REVERT: C 79 GLU cc_start: 0.8050 (tt0) cc_final: 0.7052 (mm-30) REVERT: C 222 ARG cc_start: 0.7866 (ptp-170) cc_final: 0.7344 (mtm-85) REVERT: C 238 LYS cc_start: 0.7153 (ttpp) cc_final: 0.6810 (ttmm) REVERT: C 257 ASP cc_start: 0.7977 (m-30) cc_final: 0.7730 (m-30) REVERT: C 340 LEU cc_start: 0.7374 (mt) cc_final: 0.7047 (tp) REVERT: C 343 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7094 (ttm) REVERT: C 361 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7697 (tttt) REVERT: C 380 MET cc_start: 0.7327 (mtm) cc_final: 0.7046 (mmp) REVERT: C 393 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5370 (mt) REVERT: C 512 ARG cc_start: 0.7379 (tpt90) cc_final: 0.7139 (tpp80) REVERT: C 551 ASN cc_start: 0.8394 (t0) cc_final: 0.8058 (t0) REVERT: C 744 LYS cc_start: 0.7244 (tptt) cc_final: 0.6947 (tptp) REVERT: C 756 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6371 (mt-10) REVERT: C 760 LEU cc_start: 0.7759 (mp) cc_final: 0.7408 (mp) REVERT: D 66 MET cc_start: 0.7972 (mmm) cc_final: 0.7657 (mmm) REVERT: D 79 GLU cc_start: 0.8048 (tt0) cc_final: 0.7056 (mm-30) REVERT: D 222 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7355 (mtm-85) REVERT: D 238 LYS cc_start: 0.7156 (ttpp) cc_final: 0.6811 (ttmm) REVERT: D 257 ASP cc_start: 0.7987 (m-30) cc_final: 0.7738 (m-30) REVERT: D 340 LEU cc_start: 0.7394 (mt) cc_final: 0.7071 (tp) REVERT: D 343 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7091 (ttm) REVERT: D 361 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7711 (tttt) REVERT: D 380 MET cc_start: 0.7311 (mtm) cc_final: 0.7030 (mmp) REVERT: D 393 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5411 (mt) REVERT: D 512 ARG cc_start: 0.7348 (tpt90) cc_final: 0.7126 (tpp80) REVERT: D 551 ASN cc_start: 0.8474 (t0) cc_final: 0.8142 (t0) REVERT: D 744 LYS cc_start: 0.7234 (tptt) cc_final: 0.6937 (tptp) REVERT: D 756 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6430 (mt-10) REVERT: D 760 LEU cc_start: 0.7723 (mp) cc_final: 0.7381 (mp) outliers start: 41 outliers final: 4 residues processed: 342 average time/residue: 0.5756 time to fit residues: 224.1616 Evaluate side-chains 305 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 289 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 10.0000 chunk 114 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 573 GLN A 711 GLN B 247 GLN B 573 GLN B 711 GLN C 247 GLN C 711 GLN D 247 GLN D 573 GLN D 711 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110325 restraints weight = 24035.555| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.07 r_work: 0.3160 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 22996 Z= 0.314 Angle : 0.622 7.220 31072 Z= 0.310 Chirality : 0.043 0.159 3468 Planarity : 0.005 0.048 3812 Dihedral : 13.730 177.431 3612 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.94 % Allowed : 13.09 % Favored : 83.98 % 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 aren not related in a simple way. whole: 2.06 (0.16), residues: 2628 helix: 1.87 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.09 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 260 TYR 0.023 0.002 TYR A 524 PHE 0.015 0.002 PHE C 341 TRP 0.018 0.002 TRP B 315 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00769 (22976) covalent geometry : angle 0.62202 (31052) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.61603 ( 8) hydrogen bonds : bond 0.05617 ( 1484) hydrogen bonds : angle 4.00754 ( 4344) metal coordination : bond 0.00706 ( 16) metal coordination : angle 0.79596 ( 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: 70 poor density : 308 time to evaluate : 0.691 Fit side-chains REVERT: A 21 GLN cc_start: 0.7148 (pt0) cc_final: 0.6925 (mt0) REVERT: A 66 MET cc_start: 0.7822 (mmm) cc_final: 0.7590 (mmm) REVERT: A 79 GLU cc_start: 0.7999 (tt0) cc_final: 0.7011 (mm-30) REVERT: A 222 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7440 (mtm-85) REVERT: A 238 LYS cc_start: 0.7313 (ttpp) cc_final: 0.6965 (ttmm) REVERT: A 257 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: A 331 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7054 (tm) REVERT: A 361 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7739 (tttt) REVERT: A 380 MET cc_start: 0.7406 (mtm) cc_final: 0.7158 (mmp) REVERT: A 382 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 393 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5372 (mt) REVERT: A 510 LEU cc_start: 0.6971 (mt) cc_final: 0.6561 (tt) REVERT: A 512 ARG cc_start: 0.7824 (tpt90) cc_final: 0.7404 (tpp80) REVERT: A 516 ASP cc_start: 0.7029 (m-30) cc_final: 0.6778 (m-30) REVERT: A 551 ASN cc_start: 0.8678 (t0) cc_final: 0.8377 (t0) REVERT: A 728 MET cc_start: 0.7340 (mmt) cc_final: 0.6861 (mmp) REVERT: A 744 LYS cc_start: 0.7437 (tptt) cc_final: 0.7199 (tptp) REVERT: A 756 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 21 GLN cc_start: 0.7153 (pt0) cc_final: 0.6926 (mt0) REVERT: B 66 MET cc_start: 0.7823 (mmm) cc_final: 0.7593 (mmm) REVERT: B 79 GLU cc_start: 0.8028 (tt0) cc_final: 0.7044 (mm-30) REVERT: B 222 ARG cc_start: 0.8063 (ptp-170) cc_final: 0.7438 (mtm-85) REVERT: B 238 LYS cc_start: 0.7348 (ttpp) cc_final: 0.6981 (ttmm) REVERT: B 257 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: B 331 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7050 (tm) REVERT: B 380 MET cc_start: 0.7405 (mtm) cc_final: 0.7165 (mmp) REVERT: B 382 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 393 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5372 (mt) REVERT: B 510 LEU cc_start: 0.6962 (mt) cc_final: 0.6570 (tt) REVERT: B 512 ARG cc_start: 0.7762 (tpt90) cc_final: 0.7330 (tpp80) REVERT: B 551 ASN cc_start: 0.8679 (t0) cc_final: 0.8397 (t0) REVERT: B 570 GLU cc_start: 0.8565 (tp30) cc_final: 0.8262 (mm-30) REVERT: B 728 MET cc_start: 0.7356 (mmt) cc_final: 0.6874 (mmp) REVERT: B 744 LYS cc_start: 0.7422 (tptt) cc_final: 0.7186 (tptp) REVERT: B 756 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6833 (mt-10) REVERT: C 21 GLN cc_start: 0.7146 (pt0) cc_final: 0.6915 (mt0) REVERT: C 79 GLU cc_start: 0.8014 (tt0) cc_final: 0.7039 (mm-30) REVERT: C 222 ARG cc_start: 0.8073 (ptp-170) cc_final: 0.7442 (mtm-85) REVERT: C 238 LYS cc_start: 0.7342 (ttpp) cc_final: 0.6976 (ttmm) REVERT: C 257 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: C 361 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7723 (tttt) REVERT: C 380 MET cc_start: 0.7395 (mtm) cc_final: 0.7157 (mmp) REVERT: C 382 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7522 (mp) REVERT: C 393 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5361 (mt) REVERT: C 510 LEU cc_start: 0.6943 (mt) cc_final: 0.6550 (tt) REVERT: C 512 ARG cc_start: 0.7749 (tpt90) cc_final: 0.7318 (tpp80) REVERT: C 551 ASN cc_start: 0.8675 (t0) cc_final: 0.8369 (t0) REVERT: C 728 MET cc_start: 0.7349 (mmt) cc_final: 0.6872 (mmp) REVERT: C 744 LYS cc_start: 0.7417 (tptt) cc_final: 0.7182 (tptp) REVERT: C 756 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6756 (mt-10) REVERT: C 760 LEU cc_start: 0.7792 (mp) cc_final: 0.7428 (mp) REVERT: D 21 GLN cc_start: 0.7148 (pt0) cc_final: 0.6922 (mt0) REVERT: D 66 MET cc_start: 0.7835 (mmm) cc_final: 0.7597 (mmm) REVERT: D 79 GLU cc_start: 0.8008 (tt0) cc_final: 0.7026 (mm-30) REVERT: D 222 ARG cc_start: 0.8052 (ptp-170) cc_final: 0.7423 (mtm-85) REVERT: D 238 LYS cc_start: 0.7323 (ttpp) cc_final: 0.6958 (ttmm) REVERT: D 257 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: D 361 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7723 (tttt) REVERT: D 380 MET cc_start: 0.7395 (mtm) cc_final: 0.7152 (mmp) REVERT: D 382 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7520 (mp) REVERT: D 393 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5409 (mt) REVERT: D 510 LEU cc_start: 0.6982 (mt) cc_final: 0.6582 (tt) REVERT: D 512 ARG cc_start: 0.7742 (tpt90) cc_final: 0.7320 (tpp80) REVERT: D 551 ASN cc_start: 0.8674 (t0) cc_final: 0.8390 (t0) REVERT: D 728 MET cc_start: 0.7345 (mmt) cc_final: 0.6871 (mmp) REVERT: D 744 LYS cc_start: 0.7447 (tptt) cc_final: 0.7208 (tptp) REVERT: D 756 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6793 (mt-10) REVERT: D 760 LEU cc_start: 0.7773 (mp) cc_final: 0.7404 (mp) outliers start: 70 outliers final: 16 residues processed: 352 average time/residue: 0.5299 time to fit residues: 213.7274 Evaluate side-chains 322 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 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 108 VAL 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 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 160 LEU 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 515 LEU 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: 0.6980 chunk 189 optimal weight: 1.9990 chunk 181 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 255 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 141 optimal weight: 7.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN C 247 GLN D 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116260 restraints weight = 24077.373| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.19 r_work: 0.3244 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22996 Z= 0.099 Angle : 0.432 7.817 31072 Z= 0.219 Chirality : 0.034 0.148 3468 Planarity : 0.003 0.048 3812 Dihedral : 12.396 178.881 3612 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 14.60 % Favored : 83.14 % 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 aren not related in a simple way. whole: 2.75 (0.16), residues: 2628 helix: 2.43 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.02 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 191 TYR 0.014 0.001 TYR C 348 PHE 0.023 0.001 PHE A 427 TRP 0.012 0.001 TRP C 315 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00209 (22976) covalent geometry : angle 0.43169 (31052) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.49488 ( 8) hydrogen bonds : bond 0.03719 ( 1484) hydrogen bonds : angle 3.65162 ( 4344) metal coordination : bond 0.00266 ( 16) metal coordination : angle 0.82869 ( 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 365 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7947 (tt0) cc_final: 0.6941 (mm-30) REVERT: A 222 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7415 (mtm-85) REVERT: A 257 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: A 331 LEU cc_start: 0.7341 (mt) cc_final: 0.7035 (tm) REVERT: A 361 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7745 (tttt) REVERT: A 380 MET cc_start: 0.7569 (mtm) cc_final: 0.7230 (mmp) REVERT: A 393 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5367 (mt) REVERT: A 422 MET cc_start: 0.7467 (tpp) cc_final: 0.6655 (ttp) REVERT: A 429 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: A 512 ARG cc_start: 0.7676 (tpt90) cc_final: 0.7304 (tpp80) REVERT: A 516 ASP cc_start: 0.6730 (m-30) cc_final: 0.6502 (m-30) REVERT: A 529 LEU cc_start: 0.8028 (tp) cc_final: 0.7774 (mt) REVERT: A 551 ASN cc_start: 0.8498 (t0) cc_final: 0.8150 (t0) REVERT: A 728 MET cc_start: 0.7256 (mmt) cc_final: 0.6648 (mmp) REVERT: A 744 LYS cc_start: 0.7408 (tptt) cc_final: 0.7199 (tptp) REVERT: A 756 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6763 (mt-10) REVERT: B 79 GLU cc_start: 0.7952 (tt0) cc_final: 0.6950 (mm-30) REVERT: B 222 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7408 (mtm-85) REVERT: B 257 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: B 331 LEU cc_start: 0.7363 (mt) cc_final: 0.7055 (tm) REVERT: B 380 MET cc_start: 0.7528 (mtm) cc_final: 0.7202 (mmp) REVERT: B 393 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5390 (mt) REVERT: B 422 MET cc_start: 0.7474 (tpp) cc_final: 0.6666 (ttp) REVERT: B 429 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: B 512 ARG cc_start: 0.7615 (tpt90) cc_final: 0.7219 (tpp80) REVERT: B 529 LEU cc_start: 0.8025 (tp) cc_final: 0.7768 (mt) REVERT: B 551 ASN cc_start: 0.8491 (t0) cc_final: 0.8143 (t0) REVERT: B 570 GLU cc_start: 0.8557 (tp30) cc_final: 0.8348 (mm-30) REVERT: B 728 MET cc_start: 0.7256 (mmt) cc_final: 0.6648 (mmp) REVERT: B 744 LYS cc_start: 0.7431 (tptt) cc_final: 0.7221 (tptp) REVERT: B 756 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6724 (mt-10) REVERT: C 79 GLU cc_start: 0.7949 (tt0) cc_final: 0.6947 (mm-30) REVERT: C 222 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7412 (mtm-85) REVERT: C 257 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: C 361 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7794 (tttt) REVERT: C 380 MET cc_start: 0.7572 (mtm) cc_final: 0.7217 (mmp) REVERT: C 382 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7399 (mp) REVERT: C 393 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5389 (mt) REVERT: C 422 MET cc_start: 0.7448 (tpp) cc_final: 0.6650 (ttp) REVERT: C 512 ARG cc_start: 0.7621 (tpt90) cc_final: 0.7200 (tpp80) REVERT: C 529 LEU cc_start: 0.8041 (tp) cc_final: 0.7779 (mt) REVERT: C 551 ASN cc_start: 0.8495 (t0) cc_final: 0.8147 (t0) REVERT: C 728 MET cc_start: 0.7257 (mmt) cc_final: 0.6648 (mmp) REVERT: C 744 LYS cc_start: 0.7419 (tptt) cc_final: 0.7210 (tptp) REVERT: C 756 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6747 (mt-10) REVERT: D 79 GLU cc_start: 0.7967 (tt0) cc_final: 0.6968 (mm-30) REVERT: D 222 ARG cc_start: 0.7934 (ptp-170) cc_final: 0.7414 (mtm-85) REVERT: D 257 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: D 361 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7790 (tttt) REVERT: D 380 MET cc_start: 0.7560 (mtm) cc_final: 0.7222 (mmp) REVERT: D 382 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7390 (mp) REVERT: D 393 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5367 (mt) REVERT: D 422 MET cc_start: 0.7452 (tpp) cc_final: 0.6615 (ttp) REVERT: D 429 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: D 512 ARG cc_start: 0.7588 (tpt90) cc_final: 0.7174 (tpp80) REVERT: D 529 LEU cc_start: 0.8026 (tp) cc_final: 0.7766 (mt) REVERT: D 551 ASN cc_start: 0.8494 (t0) cc_final: 0.8143 (t0) REVERT: D 728 MET cc_start: 0.7209 (mmt) cc_final: 0.6608 (mmp) REVERT: D 744 LYS cc_start: 0.7421 (tptt) cc_final: 0.7211 (tptp) REVERT: D 756 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6752 (mt-10) outliers start: 54 outliers final: 7 residues processed: 352 average time/residue: 0.5129 time to fit residues: 207.9812 Evaluate side-chains 307 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 429 GLU 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 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 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 393 LEU Chi-restraints excluded: chain D residue 429 GLU 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: 5.9990 chunk 97 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 533 ASN B 326 HIS B 533 ASN C 326 HIS C 533 ASN C 742 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 = 0.3839 r_free = 0.3839 target = 0.157664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112064 restraints weight = 23802.084| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.17 r_work: 0.3188 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22996 Z= 0.182 Angle : 0.501 7.711 31072 Z= 0.252 Chirality : 0.037 0.157 3468 Planarity : 0.004 0.050 3812 Dihedral : 12.326 176.265 3612 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.10 % Allowed : 14.26 % Favored : 82.63 % 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 aren not related in a simple way. whole: 2.52 (0.16), residues: 2628 helix: 2.26 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.10 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 557 TYR 0.019 0.001 TYR A 524 PHE 0.016 0.002 PHE D 341 TRP 0.014 0.001 TRP A 315 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00438 (22976) covalent geometry : angle 0.50075 (31052) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.50618 ( 8) hydrogen bonds : bond 0.04509 ( 1484) hydrogen bonds : angle 3.72559 ( 4344) metal coordination : bond 0.00418 ( 16) metal coordination : angle 0.50713 ( 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 387 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 313 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8005 (tt0) cc_final: 0.7045 (mm-30) REVERT: A 81 GLU cc_start: 0.6516 (mt-10) cc_final: 0.5955 (tm-30) REVERT: A 222 ARG cc_start: 0.8056 (ptp-170) cc_final: 0.7462 (mtm-85) REVERT: A 238 LYS cc_start: 0.7620 (ttpp) cc_final: 0.7267 (ttmm) REVERT: A 257 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: A 331 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7018 (tm) REVERT: A 361 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7752 (tttt) REVERT: A 380 MET cc_start: 0.7610 (mtm) cc_final: 0.7279 (mmp) REVERT: A 382 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7467 (mp) REVERT: A 393 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5350 (mt) REVERT: A 422 MET cc_start: 0.7518 (tpp) cc_final: 0.6777 (ttp) REVERT: A 512 ARG cc_start: 0.7831 (tpt90) cc_final: 0.7339 (tpp80) REVERT: A 516 ASP cc_start: 0.6880 (m-30) cc_final: 0.6672 (m-30) REVERT: A 529 LEU cc_start: 0.8147 (tp) cc_final: 0.7881 (mt) REVERT: A 551 ASN cc_start: 0.8573 (t0) cc_final: 0.8217 (t0) REVERT: A 728 MET cc_start: 0.7362 (mmt) cc_final: 0.6743 (mmp) REVERT: A 744 LYS cc_start: 0.7518 (tptt) cc_final: 0.7273 (tptp) REVERT: A 756 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6836 (mt-10) REVERT: B 79 GLU cc_start: 0.8007 (tt0) cc_final: 0.7038 (mm-30) REVERT: B 81 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5965 (tm-30) REVERT: B 222 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7529 (mtm-85) REVERT: B 238 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7224 (ttmm) REVERT: B 257 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: B 331 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7010 (tm) REVERT: B 380 MET cc_start: 0.7640 (mtm) cc_final: 0.7311 (mmp) REVERT: B 382 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 393 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5368 (mt) REVERT: B 422 MET cc_start: 0.7515 (tpp) cc_final: 0.6782 (ttp) REVERT: B 512 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7320 (tpp80) REVERT: B 529 LEU cc_start: 0.8141 (tp) cc_final: 0.7875 (mt) REVERT: B 551 ASN cc_start: 0.8552 (t0) cc_final: 0.8191 (t0) REVERT: B 570 GLU cc_start: 0.8622 (tp30) cc_final: 0.8326 (mm-30) REVERT: B 728 MET cc_start: 0.7358 (mmt) cc_final: 0.6742 (mmp) REVERT: B 744 LYS cc_start: 0.7510 (tptt) cc_final: 0.7265 (tptp) REVERT: B 756 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6813 (mt-10) REVERT: C 79 GLU cc_start: 0.8010 (tt0) cc_final: 0.7063 (mm-30) REVERT: C 81 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5952 (tm-30) REVERT: C 222 ARG cc_start: 0.8060 (ptp-170) cc_final: 0.7527 (mtm-85) REVERT: C 238 LYS cc_start: 0.7564 (ttpp) cc_final: 0.7210 (ttmm) REVERT: C 257 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: C 361 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7831 (tttt) REVERT: C 380 MET cc_start: 0.7632 (mtm) cc_final: 0.7307 (mmp) REVERT: C 382 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 393 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5334 (mt) REVERT: C 422 MET cc_start: 0.7544 (tpp) cc_final: 0.6696 (ttp) REVERT: C 427 PHE cc_start: 0.6730 (t80) cc_final: 0.6490 (t80) REVERT: C 512 ARG cc_start: 0.7807 (tpt90) cc_final: 0.7313 (tpp80) REVERT: C 529 LEU cc_start: 0.8144 (tp) cc_final: 0.7871 (mt) REVERT: C 551 ASN cc_start: 0.8555 (t0) cc_final: 0.8196 (t0) REVERT: C 728 MET cc_start: 0.7371 (mmt) cc_final: 0.6756 (mmp) REVERT: C 744 LYS cc_start: 0.7504 (tptt) cc_final: 0.7260 (tptp) REVERT: C 756 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 79 GLU cc_start: 0.8025 (tt0) cc_final: 0.7069 (mm-30) REVERT: D 81 GLU cc_start: 0.6517 (mt-10) cc_final: 0.5959 (tm-30) REVERT: D 222 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7527 (mtm-85) REVERT: D 238 LYS cc_start: 0.7536 (ttpp) cc_final: 0.7207 (ttmm) REVERT: D 257 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: D 361 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7822 (tttt) REVERT: D 380 MET cc_start: 0.7635 (mtm) cc_final: 0.7309 (mmp) REVERT: D 382 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7511 (mp) REVERT: D 393 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5346 (mt) REVERT: D 422 MET cc_start: 0.7553 (tpp) cc_final: 0.6811 (ttp) REVERT: D 512 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7307 (tpp80) REVERT: D 529 LEU cc_start: 0.8141 (tp) cc_final: 0.7872 (mt) REVERT: D 551 ASN cc_start: 0.8567 (t0) cc_final: 0.8209 (t0) REVERT: D 728 MET cc_start: 0.7350 (mmt) cc_final: 0.6730 (mmp) REVERT: D 744 LYS cc_start: 0.7515 (tptt) cc_final: 0.7269 (tptp) REVERT: D 756 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6827 (mt-10) outliers start: 74 outliers final: 23 residues processed: 361 average time/residue: 0.5063 time to fit residues: 210.5661 Evaluate side-chains 341 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 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 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 250 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 356 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 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 356 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: 0.9980 chunk 181 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 533 ASN B 326 HIS B 533 ASN C 326 HIS C 533 ASN D 326 HIS D 533 ASN D 742 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114538 restraints weight = 23884.374| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.18 r_work: 0.3227 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22996 Z= 0.108 Angle : 0.454 8.124 31072 Z= 0.229 Chirality : 0.034 0.154 3468 Planarity : 0.003 0.049 3812 Dihedral : 11.633 178.405 3612 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.89 % Allowed : 15.56 % Favored : 82.55 % 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 aren not related in a simple way. whole: 2.77 (0.16), residues: 2628 helix: 2.45 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.05 (0.23), residues: 660 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 520 TRP 0.015 0.001 TRP C 315 HIS 0.002 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00241 (22976) covalent geometry : angle 0.45448 (31052) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.37354 ( 8) hydrogen bonds : bond 0.03862 ( 1484) hydrogen bonds : angle 3.62419 ( 4344) metal coordination : bond 0.00236 ( 16) metal coordination : angle 0.47821 ( 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 341 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7939 (tt0) cc_final: 0.6962 (mm-30) REVERT: A 81 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5892 (tm-30) REVERT: A 222 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7549 (mtm110) REVERT: A 257 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: A 331 LEU cc_start: 0.7277 (mt) cc_final: 0.6963 (tm) REVERT: A 361 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7696 (tttt) REVERT: A 380 MET cc_start: 0.7538 (mtm) cc_final: 0.7242 (mmp) REVERT: A 393 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5290 (mt) REVERT: A 422 MET cc_start: 0.7469 (tpp) cc_final: 0.6897 (ttp) REVERT: A 512 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7280 (tpp80) REVERT: A 529 LEU cc_start: 0.8048 (tp) cc_final: 0.7791 (mt) REVERT: A 551 ASN cc_start: 0.8520 (t0) cc_final: 0.8143 (t0) REVERT: A 728 MET cc_start: 0.7242 (mmt) cc_final: 0.6584 (mmp) REVERT: A 744 LYS cc_start: 0.7497 (tptt) cc_final: 0.7271 (tptp) REVERT: A 756 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6786 (mt-10) REVERT: B 79 GLU cc_start: 0.7952 (tt0) cc_final: 0.6977 (mm-30) REVERT: B 81 GLU cc_start: 0.6508 (mt-10) cc_final: 0.5902 (tm-30) REVERT: B 222 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7541 (mtm110) REVERT: B 257 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: B 331 LEU cc_start: 0.7259 (mt) cc_final: 0.6940 (tm) REVERT: B 380 MET cc_start: 0.7520 (mtm) cc_final: 0.7231 (mmp) REVERT: B 393 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5359 (mt) REVERT: B 422 MET cc_start: 0.7472 (tpp) cc_final: 0.6904 (ttp) REVERT: B 512 ARG cc_start: 0.7806 (tpt90) cc_final: 0.7269 (tpp80) REVERT: B 529 LEU cc_start: 0.8053 (tp) cc_final: 0.7799 (mt) REVERT: B 551 ASN cc_start: 0.8495 (t0) cc_final: 0.8114 (t0) REVERT: B 570 GLU cc_start: 0.8513 (tp30) cc_final: 0.8192 (mm-30) REVERT: B 728 MET cc_start: 0.7227 (mmt) cc_final: 0.6573 (mmp) REVERT: B 744 LYS cc_start: 0.7495 (tptt) cc_final: 0.7268 (tptp) REVERT: B 756 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6801 (mt-10) REVERT: C 79 GLU cc_start: 0.7957 (tt0) cc_final: 0.6983 (mm-30) REVERT: C 81 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5900 (tm-30) REVERT: C 222 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.7562 (mtm110) REVERT: C 257 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: C 380 MET cc_start: 0.7516 (mtm) cc_final: 0.7231 (mmp) REVERT: C 393 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5345 (mt) REVERT: C 422 MET cc_start: 0.7490 (tpp) cc_final: 0.6680 (ttp) REVERT: C 512 ARG cc_start: 0.7810 (tpt90) cc_final: 0.7273 (tpp80) REVERT: C 529 LEU cc_start: 0.8061 (tp) cc_final: 0.7800 (mt) REVERT: C 551 ASN cc_start: 0.8503 (t0) cc_final: 0.8123 (t0) REVERT: C 728 MET cc_start: 0.7255 (mmt) cc_final: 0.6599 (mmp) REVERT: C 744 LYS cc_start: 0.7491 (tptt) cc_final: 0.7266 (tptp) REVERT: C 756 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6771 (mt-10) REVERT: D 79 GLU cc_start: 0.7969 (tt0) cc_final: 0.6992 (mm-30) REVERT: D 81 GLU cc_start: 0.6508 (mt-10) cc_final: 0.5904 (tm-30) REVERT: D 222 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7552 (mtm110) REVERT: D 257 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: D 361 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7777 (tttt) REVERT: D 380 MET cc_start: 0.7517 (mtm) cc_final: 0.7230 (mmp) REVERT: D 393 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5337 (mt) REVERT: D 422 MET cc_start: 0.7473 (tpp) cc_final: 0.6624 (ttp) REVERT: D 512 ARG cc_start: 0.7791 (tpt90) cc_final: 0.7258 (tpp80) REVERT: D 529 LEU cc_start: 0.8069 (tp) cc_final: 0.7808 (mt) REVERT: D 551 ASN cc_start: 0.8529 (t0) cc_final: 0.8152 (t0) REVERT: D 728 MET cc_start: 0.7231 (mmt) cc_final: 0.6577 (mmp) REVERT: D 744 LYS cc_start: 0.7492 (tptt) cc_final: 0.7263 (tptp) REVERT: D 756 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6789 (mt-10) outliers start: 45 outliers final: 14 residues processed: 333 average time/residue: 0.5042 time to fit residues: 193.8644 Evaluate side-chains 309 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP 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 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 257 ASP 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 361 LYS 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 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: 20.0000 chunk 210 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 533 ASN A 709 GLN B 326 HIS B 533 ASN B 709 GLN C 326 HIS C 533 ASN C 709 GLN D 326 HIS D 533 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110492 restraints weight = 24063.217| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.19 r_work: 0.3151 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 22996 Z= 0.239 Angle : 0.557 8.210 31072 Z= 0.278 Chirality : 0.039 0.156 3468 Planarity : 0.004 0.050 3812 Dihedral : 12.078 174.340 3612 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.35 % Allowed : 15.73 % Favored : 81.92 % 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 aren not related in a simple way. whole: 2.27 (0.16), residues: 2628 helix: 2.07 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.18 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 464 TYR 0.022 0.002 TYR A 524 PHE 0.023 0.002 PHE C 427 TRP 0.014 0.002 TRP A 315 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00584 (22976) covalent geometry : angle 0.55721 (31052) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.53900 ( 8) hydrogen bonds : bond 0.04982 ( 1484) hydrogen bonds : angle 3.82399 ( 4344) metal coordination : bond 0.00459 ( 16) metal coordination : angle 0.58195 ( 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 362 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8002 (tt0) cc_final: 0.7077 (mm-30) REVERT: A 81 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6015 (tm-30) REVERT: A 222 ARG cc_start: 0.8089 (ptp-170) cc_final: 0.7419 (mtm-85) REVERT: A 238 LYS cc_start: 0.7601 (ttpp) cc_final: 0.7249 (ttmm) REVERT: A 257 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: A 331 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6973 (tm) REVERT: A 380 MET cc_start: 0.7537 (mtm) cc_final: 0.7222 (mmp) REVERT: A 393 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5404 (mt) REVERT: A 422 MET cc_start: 0.7527 (tpp) cc_final: 0.6781 (ttp) REVERT: A 510 LEU cc_start: 0.7116 (mt) cc_final: 0.6746 (tt) REVERT: A 512 ARG cc_start: 0.8015 (tpt90) cc_final: 0.7413 (tpp80) REVERT: A 529 LEU cc_start: 0.8143 (tp) cc_final: 0.7878 (mt) REVERT: A 728 MET cc_start: 0.7390 (mmt) cc_final: 0.6794 (mmp) REVERT: A 756 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 79 GLU cc_start: 0.8017 (tt0) cc_final: 0.7084 (mm-30) REVERT: B 81 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6024 (tm-30) REVERT: B 222 ARG cc_start: 0.8092 (ptp-170) cc_final: 0.7425 (mtm-85) REVERT: B 238 LYS cc_start: 0.7601 (ttpp) cc_final: 0.7259 (ttmm) REVERT: B 257 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 331 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6959 (tm) REVERT: B 380 MET cc_start: 0.7500 (mtm) cc_final: 0.7229 (mmp) REVERT: B 393 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5394 (mt) REVERT: B 422 MET cc_start: 0.7521 (tpp) cc_final: 0.6783 (ttp) REVERT: B 510 LEU cc_start: 0.7130 (mt) cc_final: 0.6743 (tt) REVERT: B 512 ARG cc_start: 0.8017 (tpt90) cc_final: 0.7389 (tpp80) REVERT: B 529 LEU cc_start: 0.8169 (tp) cc_final: 0.7910 (mt) REVERT: B 570 GLU cc_start: 0.8609 (tp30) cc_final: 0.8292 (mm-30) REVERT: B 625 ASN cc_start: 0.8286 (m110) cc_final: 0.8001 (m110) REVERT: B 728 MET cc_start: 0.7391 (mmt) cc_final: 0.6801 (mmp) REVERT: B 756 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6891 (mt-10) REVERT: C 79 GLU cc_start: 0.8017 (tt0) cc_final: 0.7088 (mm-30) REVERT: C 81 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6000 (tm-30) REVERT: C 222 ARG cc_start: 0.8094 (ptp-170) cc_final: 0.7431 (mtm-85) REVERT: C 238 LYS cc_start: 0.7602 (ttpp) cc_final: 0.7258 (ttmm) REVERT: C 257 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: C 380 MET cc_start: 0.7539 (mtm) cc_final: 0.7231 (mmp) REVERT: C 393 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5402 (mt) REVERT: C 422 MET cc_start: 0.7523 (tpp) cc_final: 0.6754 (ttp) REVERT: C 510 LEU cc_start: 0.7122 (mt) cc_final: 0.6733 (tt) REVERT: C 512 ARG cc_start: 0.8007 (tpt90) cc_final: 0.7381 (tpp80) REVERT: C 529 LEU cc_start: 0.8142 (tp) cc_final: 0.7873 (mt) REVERT: C 728 MET cc_start: 0.7392 (mmt) cc_final: 0.6798 (mmp) REVERT: C 756 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6937 (mt-10) REVERT: D 79 GLU cc_start: 0.8022 (tt0) cc_final: 0.7090 (mm-30) REVERT: D 81 GLU cc_start: 0.6543 (mt-10) cc_final: 0.5999 (tm-30) REVERT: D 222 ARG cc_start: 0.8088 (ptp-170) cc_final: 0.7416 (mtm-85) REVERT: D 238 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7246 (ttmm) REVERT: D 257 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: D 380 MET cc_start: 0.7534 (mtm) cc_final: 0.7229 (mmp) REVERT: D 393 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5405 (mt) REVERT: D 422 MET cc_start: 0.7533 (tpp) cc_final: 0.6708 (ttp) REVERT: D 510 LEU cc_start: 0.7094 (mt) cc_final: 0.6716 (tt) REVERT: D 512 ARG cc_start: 0.7990 (tpt90) cc_final: 0.7367 (tpp80) REVERT: D 529 LEU cc_start: 0.8143 (tp) cc_final: 0.7879 (mt) REVERT: D 728 MET cc_start: 0.7371 (mmt) cc_final: 0.6776 (mmp) REVERT: D 756 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6921 (mt-10) outliers start: 56 outliers final: 16 residues processed: 343 average time/residue: 0.5342 time to fit residues: 211.1696 Evaluate side-chains 323 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 297 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 257 ASP 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 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: 5.9990 chunk 2 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 231 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 533 ASN A 709 GLN A 742 ASN B 326 HIS B 533 ASN B 709 GLN B 742 ASN C 309 GLN C 326 HIS C 533 ASN C 709 GLN D 326 HIS D 533 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114891 restraints weight = 23769.995| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.17 r_work: 0.3229 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22996 Z= 0.110 Angle : 0.469 8.495 31072 Z= 0.235 Chirality : 0.035 0.154 3468 Planarity : 0.003 0.050 3812 Dihedral : 11.358 177.397 3612 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.68 % Allowed : 16.69 % Favored : 81.63 % 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 aren not related in a simple way. whole: 2.69 (0.16), residues: 2628 helix: 2.39 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.11 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 593 TYR 0.011 0.001 TYR D 524 PHE 0.020 0.001 PHE C 427 TRP 0.016 0.001 TRP C 315 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00247 (22976) covalent geometry : angle 0.46951 (31052) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.40246 ( 8) hydrogen bonds : bond 0.03843 ( 1484) hydrogen bonds : angle 3.64023 ( 4344) metal coordination : bond 0.00193 ( 16) metal coordination : angle 0.48412 ( 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 325 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7948 (tt0) cc_final: 0.6984 (mm-30) REVERT: A 81 GLU cc_start: 0.6606 (mt-10) cc_final: 0.5963 (tm-30) REVERT: A 170 ARG cc_start: 0.7863 (ttm170) cc_final: 0.6566 (pmt170) REVERT: A 222 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7477 (mtm110) REVERT: A 257 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: A 331 LEU cc_start: 0.7218 (mt) cc_final: 0.6910 (tm) REVERT: A 361 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7715 (tttt) REVERT: A 380 MET cc_start: 0.7415 (mtm) cc_final: 0.7178 (mmp) REVERT: A 393 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5324 (mt) REVERT: A 422 MET cc_start: 0.7510 (tpp) cc_final: 0.6919 (ttp) REVERT: A 512 ARG cc_start: 0.7940 (tpt90) cc_final: 0.7317 (tpp80) REVERT: A 529 LEU cc_start: 0.8040 (tp) cc_final: 0.7802 (mt) REVERT: A 728 MET cc_start: 0.7261 (mmt) cc_final: 0.6625 (mmp) REVERT: A 756 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6847 (mt-10) REVERT: B 79 GLU cc_start: 0.7945 (tt0) cc_final: 0.6990 (mm-30) REVERT: B 81 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5973 (tm-30) REVERT: B 222 ARG cc_start: 0.7942 (ptp-170) cc_final: 0.7510 (mtm-85) REVERT: B 257 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: B 331 LEU cc_start: 0.7217 (mt) cc_final: 0.6910 (tm) REVERT: B 361 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7572 (tttt) REVERT: B 380 MET cc_start: 0.7400 (mtm) cc_final: 0.7168 (mmp) REVERT: B 393 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5346 (mt) REVERT: B 422 MET cc_start: 0.7499 (tpp) cc_final: 0.6908 (ttp) REVERT: B 512 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7289 (tpp80) REVERT: B 529 LEU cc_start: 0.8049 (tp) cc_final: 0.7814 (mt) REVERT: B 570 GLU cc_start: 0.8512 (tp30) cc_final: 0.8280 (mm-30) REVERT: B 728 MET cc_start: 0.7270 (mmt) cc_final: 0.6637 (mmp) REVERT: B 756 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6844 (mt-10) REVERT: C 79 GLU cc_start: 0.7960 (tt0) cc_final: 0.7008 (mm-30) REVERT: C 81 GLU cc_start: 0.6572 (mt-10) cc_final: 0.5969 (tm-30) REVERT: C 170 ARG cc_start: 0.7851 (ttm170) cc_final: 0.6564 (pmt170) REVERT: C 222 ARG cc_start: 0.7960 (ptp-170) cc_final: 0.7525 (mtm-85) REVERT: C 257 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: C 380 MET cc_start: 0.7409 (mtm) cc_final: 0.7181 (mmp) REVERT: C 393 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5302 (mt) REVERT: C 422 MET cc_start: 0.7475 (tpp) cc_final: 0.6796 (ttp) REVERT: C 512 ARG cc_start: 0.7959 (tpt90) cc_final: 0.7325 (tpp80) REVERT: C 529 LEU cc_start: 0.8046 (tp) cc_final: 0.7802 (mt) REVERT: C 728 MET cc_start: 0.7281 (mmt) cc_final: 0.6644 (mmp) REVERT: C 756 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6845 (mt-10) REVERT: D 79 GLU cc_start: 0.7958 (tt0) cc_final: 0.7007 (mm-30) REVERT: D 81 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5972 (tm-30) REVERT: D 170 ARG cc_start: 0.7859 (ttm170) cc_final: 0.6565 (pmt170) REVERT: D 222 ARG cc_start: 0.7952 (ptp-170) cc_final: 0.7474 (mtm110) REVERT: D 257 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: D 380 MET cc_start: 0.7405 (mtm) cc_final: 0.7175 (mmp) REVERT: D 393 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5361 (mt) REVERT: D 422 MET cc_start: 0.7520 (tpp) cc_final: 0.6932 (ttp) REVERT: D 512 ARG cc_start: 0.7946 (tpt90) cc_final: 0.7274 (tpp80) REVERT: D 529 LEU cc_start: 0.8046 (tp) cc_final: 0.7802 (mt) REVERT: D 728 MET cc_start: 0.7266 (mmt) cc_final: 0.6631 (mmp) REVERT: D 756 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6856 (mt-10) outliers start: 40 outliers final: 14 residues processed: 321 average time/residue: 0.5023 time to fit residues: 185.6996 Evaluate side-chains 306 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP 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 361 LYS 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 257 ASP 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 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER 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: 3.9990 chunk 205 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 326 HIS C 326 HIS D 326 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115148 restraints weight = 23882.221| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.19 r_work: 0.3236 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: 0.7610 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22996 Z= 0.109 Angle : 0.459 8.718 31072 Z= 0.229 Chirality : 0.034 0.154 3468 Planarity : 0.004 0.050 3812 Dihedral : 10.854 175.728 3612 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.43 % Allowed : 16.61 % Favored : 81.96 % 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 aren not related in a simple way. whole: 2.89 (0.16), residues: 2628 helix: 2.53 (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 593 TYR 0.013 0.001 TYR A 524 PHE 0.023 0.001 PHE C 520 TRP 0.016 0.001 TRP D 315 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00246 (22976) covalent geometry : angle 0.45951 (31052) SS BOND : bond 0.00029 ( 4) SS BOND : angle 0.30218 ( 8) hydrogen bonds : bond 0.03759 ( 1484) hydrogen bonds : angle 3.55875 ( 4344) metal coordination : bond 0.00220 ( 16) metal coordination : angle 0.43765 ( 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 326 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7975 (tt0) cc_final: 0.7047 (mm-30) REVERT: A 81 GLU cc_start: 0.6580 (mt-10) cc_final: 0.5993 (tm-30) REVERT: A 170 ARG cc_start: 0.7881 (ttm170) cc_final: 0.6597 (pmt170) REVERT: A 222 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7604 (mtm-85) REVERT: A 257 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: A 331 LEU cc_start: 0.7243 (mt) cc_final: 0.6905 (tm) REVERT: A 361 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (tttt) REVERT: A 393 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5366 (mt) REVERT: A 422 MET cc_start: 0.7495 (tpp) cc_final: 0.6890 (ttp) REVERT: A 512 ARG cc_start: 0.7983 (tpt90) cc_final: 0.7359 (tpp80) REVERT: A 529 LEU cc_start: 0.8187 (tp) cc_final: 0.7950 (mt) REVERT: A 728 MET cc_start: 0.7315 (mmt) cc_final: 0.6836 (mmp) REVERT: A 756 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 758 LEU cc_start: 0.6803 (mt) cc_final: 0.6537 (mt) REVERT: B 79 GLU cc_start: 0.7996 (tt0) cc_final: 0.7068 (mm-30) REVERT: B 81 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6010 (tm-30) REVERT: B 222 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7584 (mtm-85) REVERT: B 257 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: B 331 LEU cc_start: 0.7261 (mt) cc_final: 0.6925 (tm) REVERT: B 361 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7625 (tttt) REVERT: B 393 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5380 (mt) REVERT: B 422 MET cc_start: 0.7483 (tpp) cc_final: 0.6874 (ttp) REVERT: B 512 ARG cc_start: 0.8004 (tpt90) cc_final: 0.7363 (tpp80) REVERT: B 529 LEU cc_start: 0.8186 (tp) cc_final: 0.7952 (mt) REVERT: B 570 GLU cc_start: 0.8558 (tp30) cc_final: 0.8317 (mm-30) REVERT: B 728 MET cc_start: 0.7323 (mmt) cc_final: 0.6852 (mmp) REVERT: B 756 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6889 (mt-10) REVERT: B 758 LEU cc_start: 0.6803 (mt) cc_final: 0.6532 (mt) REVERT: C 79 GLU cc_start: 0.7992 (tt0) cc_final: 0.7066 (mm-30) REVERT: C 81 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6020 (tm-30) REVERT: C 170 ARG cc_start: 0.7864 (ttm170) cc_final: 0.6589 (pmt170) REVERT: C 222 ARG cc_start: 0.7991 (ptp-170) cc_final: 0.7599 (mtm-85) REVERT: C 393 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5393 (mt) REVERT: C 422 MET cc_start: 0.7541 (tpp) cc_final: 0.6983 (ttp) REVERT: C 512 ARG cc_start: 0.7995 (tpt90) cc_final: 0.7358 (tpp80) REVERT: C 529 LEU cc_start: 0.8183 (tp) cc_final: 0.7944 (mt) REVERT: C 728 MET cc_start: 0.7325 (mmt) cc_final: 0.6854 (mmp) REVERT: C 756 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6899 (mt-10) REVERT: C 758 LEU cc_start: 0.6815 (mt) cc_final: 0.6543 (mt) REVERT: D 79 GLU cc_start: 0.7983 (tt0) cc_final: 0.7060 (mm-30) REVERT: D 81 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6018 (tm-30) REVERT: D 170 ARG cc_start: 0.7865 (ttm170) cc_final: 0.6585 (pmt170) REVERT: D 222 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7597 (mtm-85) REVERT: D 380 MET cc_start: 0.7481 (mtm) cc_final: 0.7261 (mmp) REVERT: D 393 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5395 (mt) REVERT: D 422 MET cc_start: 0.7495 (tpp) cc_final: 0.6781 (ttp) REVERT: D 512 ARG cc_start: 0.7976 (tpt90) cc_final: 0.7348 (tpp80) REVERT: D 529 LEU cc_start: 0.8193 (tp) cc_final: 0.7948 (mt) REVERT: D 728 MET cc_start: 0.7316 (mmt) cc_final: 0.6843 (mmp) REVERT: D 756 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6912 (mt-10) REVERT: D 758 LEU cc_start: 0.6808 (mt) cc_final: 0.6536 (mt) outliers start: 34 outliers final: 15 residues processed: 319 average time/residue: 0.5695 time to fit residues: 208.6459 Evaluate side-chains 307 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP 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 361 LYS 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 652 ASP Chi-restraints excluded: chain B residue 717 ILE 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 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER 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: 3.9990 chunk 226 optimal weight: 0.4980 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: 3.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 709 GLN B 326 HIS B 709 GLN C 326 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112028 restraints weight = 24011.864| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.18 r_work: 0.3193 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2864 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= 0.184 Angle : 0.528 8.669 31072 Z= 0.262 Chirality : 0.037 0.163 3468 Planarity : 0.004 0.049 3812 Dihedral : 11.278 173.624 3612 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.68 % Allowed : 16.82 % 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 aren not related in a simple way. whole: 2.52 (0.16), residues: 2628 helix: 2.27 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.14 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 593 TYR 0.019 0.002 TYR C 524 PHE 0.018 0.002 PHE C 427 TRP 0.012 0.001 TRP B 315 HIS 0.003 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00445 (22976) covalent geometry : angle 0.52788 (31052) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.38396 ( 8) hydrogen bonds : bond 0.04496 ( 1484) hydrogen bonds : angle 3.70069 ( 4344) metal coordination : bond 0.00358 ( 16) metal coordination : angle 0.36144 ( 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 327 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7955 (tt0) cc_final: 0.7044 (mm-30) REVERT: A 81 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6028 (tm-30) REVERT: A 170 ARG cc_start: 0.7931 (ttm170) cc_final: 0.6616 (pmt170) REVERT: A 222 ARG cc_start: 0.8020 (ptp-170) cc_final: 0.7507 (mtm-85) REVERT: A 238 LYS cc_start: 0.7642 (ttpp) cc_final: 0.7305 (ttmm) REVERT: A 257 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: A 331 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6938 (tm) REVERT: A 361 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7815 (tttt) REVERT: A 393 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5249 (mt) REVERT: A 422 MET cc_start: 0.7470 (tpp) cc_final: 0.6951 (ttp) REVERT: A 512 ARG cc_start: 0.7953 (tpt90) cc_final: 0.7298 (tpp80) REVERT: A 529 LEU cc_start: 0.8103 (tp) cc_final: 0.7862 (mt) REVERT: A 728 MET cc_start: 0.7352 (mmt) cc_final: 0.6686 (mmp) REVERT: A 756 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6944 (mt-10) REVERT: A 758 LEU cc_start: 0.6947 (mt) cc_final: 0.6659 (mt) REVERT: B 79 GLU cc_start: 0.7967 (tt0) cc_final: 0.7052 (mm-30) REVERT: B 81 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6060 (tm-30) REVERT: B 222 ARG cc_start: 0.8019 (ptp-170) cc_final: 0.7506 (mtm-85) REVERT: B 238 LYS cc_start: 0.7640 (ttpp) cc_final: 0.7304 (ttmm) REVERT: B 257 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: B 331 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6933 (tm) REVERT: B 361 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7666 (tttt) REVERT: B 393 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5260 (mt) REVERT: B 422 MET cc_start: 0.7467 (tpp) cc_final: 0.6947 (ttp) REVERT: B 512 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7298 (tpp80) REVERT: B 529 LEU cc_start: 0.8181 (tp) cc_final: 0.7933 (mt) REVERT: B 570 GLU cc_start: 0.8570 (tp30) cc_final: 0.8250 (mm-30) REVERT: B 728 MET cc_start: 0.7342 (mmt) cc_final: 0.6677 (mmp) REVERT: B 756 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 758 LEU cc_start: 0.6908 (mt) cc_final: 0.6647 (mt) REVERT: C 79 GLU cc_start: 0.7980 (tt0) cc_final: 0.7072 (mm-30) REVERT: C 81 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6071 (tm-30) REVERT: C 170 ARG cc_start: 0.7841 (ttm170) cc_final: 0.6512 (pmt170) REVERT: C 222 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7521 (mtm-85) REVERT: C 238 LYS cc_start: 0.7635 (ttpp) cc_final: 0.7299 (ttmm) REVERT: C 393 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5370 (mt) REVERT: C 422 MET cc_start: 0.7553 (tpp) cc_final: 0.6798 (ttp) REVERT: C 512 ARG cc_start: 0.7952 (tpt90) cc_final: 0.7301 (tpp80) REVERT: C 529 LEU cc_start: 0.8169 (tp) cc_final: 0.7912 (mt) REVERT: C 728 MET cc_start: 0.7352 (mmt) cc_final: 0.6690 (mmp) REVERT: C 756 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6951 (mt-10) REVERT: C 758 LEU cc_start: 0.6967 (mt) cc_final: 0.6703 (mt) REVERT: D 79 GLU cc_start: 0.7983 (tt0) cc_final: 0.7069 (mm-30) REVERT: D 81 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6067 (tm-30) REVERT: D 170 ARG cc_start: 0.7858 (ttm170) cc_final: 0.6519 (pmt170) REVERT: D 222 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7511 (mtm-85) REVERT: D 238 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7312 (ttmm) REVERT: D 393 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5359 (mt) REVERT: D 422 MET cc_start: 0.7484 (tpp) cc_final: 0.6739 (ttp) REVERT: D 512 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7297 (tpp80) REVERT: D 529 LEU cc_start: 0.8164 (tp) cc_final: 0.7911 (mt) REVERT: D 728 MET cc_start: 0.7347 (mmt) cc_final: 0.6685 (mmp) REVERT: D 756 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6955 (mt-10) REVERT: D 758 LEU cc_start: 0.6961 (mt) cc_final: 0.6697 (mt) outliers start: 40 outliers final: 20 residues processed: 315 average time/residue: 0.5106 time to fit residues: 184.6237 Evaluate side-chains 316 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 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 361 LYS 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 652 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 250 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 250 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 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: 2.9990 chunk 144 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 212 optimal weight: 0.0270 chunk 263 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 709 GLN B 326 HIS B 709 GLN C 326 HIS D 326 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113551 restraints weight = 23830.875| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.17 r_work: 0.3211 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2874 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= 0.131 Angle : 0.486 8.847 31072 Z= 0.241 Chirality : 0.035 0.149 3468 Planarity : 0.004 0.050 3812 Dihedral : 10.997 174.644 3612 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 17.03 % 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 aren not related in a simple way. whole: 2.66 (0.16), residues: 2628 helix: 2.37 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.11 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 593 TYR 0.013 0.001 TYR B 524 PHE 0.018 0.001 PHE C 427 TRP 0.015 0.001 TRP B 315 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00306 (22976) covalent geometry : angle 0.48611 (31052) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.31467 ( 8) hydrogen bonds : bond 0.04030 ( 1484) hydrogen bonds : angle 3.64387 ( 4344) metal coordination : bond 0.00280 ( 16) metal coordination : angle 0.39940 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7289.18 seconds wall clock time: 124 minutes 43.91 seconds (7483.91 seconds total)