Starting phenix.real_space_refine on Sun Sep 29 20:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/09_2024/7d4p_30575.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/09_2024/7d4p_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/09_2024/7d4p_30575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/09_2024/7d4p_30575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/09_2024/7d4p_30575.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/09_2024/7d4p_30575.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, D Time building chain proxies: 13.96, per 1000 atoms: 0.62 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 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: 7.36 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 176 " pdb=" ZN B 805 " pdb="ZN ZN B 805 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 176 " pdb=" ZN C 805 " pdb="ZN ZN C 805 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 176 " pdb=" ZN D 805 " pdb="ZN ZN D 805 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 176 " Number of angles added : 12 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.9% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 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: 8.44 Time building geometry restraints manager: 8.23 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: 13687 32.83 - 65.67: 268 65.67 - 98.50: 44 98.50 - 131.34: 4 131.34 - 164.17: 8 Dihedral angle restraints: 14011 sinusoidal: 6095 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 14008 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: 2.04 - 2.61: 127 2.61 - 3.18: 19589 3.18 - 3.75: 35661 3.75 - 4.33: 49239 4.33 - 4.90: 82395 Nonbonded interactions: 187011 Sorted by model distance: nonbonded pdb=" SG CYS B 553 " pdb=" SG CYS B 558 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS D 553 " pdb=" SG CYS D 558 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS C 553 " pdb=" SG CYS C 558 " model vdw 2.036 3.760 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 ... (remaining 187006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 58.430 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.470 ------------------------------------------------------------------------------- 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 22976 Z= 0.417 Angle : 0.798 19.289 31052 Z= 0.333 Chirality : 0.036 0.224 3468 Planarity : 0.004 0.032 3812 Dihedral : 13.898 164.170 8856 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP A 315 HIS 0.002 0.000 HIS D 271 PHE 0.015 0.001 PHE A 341 TYR 0.016 0.001 TYR D 524 ARG 0.003 0.000 ARG D 196 *********************** 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 fitting. rotamer outliers: 16 poor density : 495 time to evaluate : 2.541 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: 1.3852 time to fit residues: 799.6183 Evaluate side-chains 327 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 320 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 222 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 711 GLN C 247 GLN C 573 GLN C 711 GLN D 247 GLN D 533 ASN D 573 GLN D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22976 Z= 0.258 Angle : 0.523 7.120 31052 Z= 0.261 Chirality : 0.037 0.152 3468 Planarity : 0.004 0.040 3812 Dihedral : 13.445 172.255 3618 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.01 % Allowed : 13.00 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.16), residues: 2628 helix: 2.29 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.24 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.004 0.001 HIS B 92 PHE 0.015 0.002 PHE A 341 TYR 0.017 0.002 TYR D 524 ARG 0.004 0.000 ARG A 191 *********************** 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 359 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 311 time to evaluate : 2.389 Fit side-chains REVERT: A 66 MET cc_start: 0.7952 (mmm) cc_final: 0.7723 (mmm) REVERT: A 79 GLU cc_start: 0.7973 (tt0) cc_final: 0.6915 (mm-30) REVERT: A 222 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.7304 (mtm-85) REVERT: A 238 LYS cc_start: 0.7175 (ttpp) cc_final: 0.6831 (ttmm) REVERT: A 257 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: A 380 MET cc_start: 0.7400 (mtm) cc_final: 0.7078 (mmp) REVERT: A 393 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5269 (mt) REVERT: A 512 ARG cc_start: 0.7453 (tpt90) cc_final: 0.7116 (tpp80) REVERT: A 516 ASP cc_start: 0.6749 (m-30) cc_final: 0.6529 (m-30) REVERT: A 551 ASN cc_start: 0.8472 (t0) cc_final: 0.8118 (t0) REVERT: A 728 MET cc_start: 0.7202 (mmt) cc_final: 0.6820 (mmp) REVERT: A 756 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6441 (mt-10) REVERT: A 760 LEU cc_start: 0.7628 (mp) cc_final: 0.7284 (mp) REVERT: B 79 GLU cc_start: 0.7973 (tt0) cc_final: 0.6916 (mm-30) REVERT: B 222 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7307 (mtm-85) REVERT: B 238 LYS cc_start: 0.7176 (ttpp) cc_final: 0.6833 (ttmm) REVERT: B 257 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: B 380 MET cc_start: 0.7399 (mtm) cc_final: 0.7081 (mmp) REVERT: B 393 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5263 (mt) REVERT: B 512 ARG cc_start: 0.7451 (tpt90) cc_final: 0.7114 (tpp80) REVERT: B 551 ASN cc_start: 0.8354 (t0) cc_final: 0.8058 (t0) REVERT: B 552 ASN cc_start: 0.7888 (m-40) cc_final: 0.7656 (t0) REVERT: B 570 GLU cc_start: 0.8396 (tp30) cc_final: 0.8069 (mm-30) REVERT: B 728 MET cc_start: 0.7200 (mmt) cc_final: 0.6820 (mmp) REVERT: B 756 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6427 (mt-10) REVERT: B 760 LEU cc_start: 0.7634 (mp) cc_final: 0.7269 (mp) REVERT: C 79 GLU cc_start: 0.7972 (tt0) cc_final: 0.6918 (mm-30) REVERT: C 222 ARG cc_start: 0.7841 (ptp-170) cc_final: 0.7306 (mtm-85) REVERT: C 238 LYS cc_start: 0.7175 (ttpp) cc_final: 0.6833 (ttmm) REVERT: C 257 ASP cc_start: 0.7993 (m-30) cc_final: 0.7759 (m-30) REVERT: C 343 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.7105 (ttm) REVERT: C 361 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7573 (tttt) REVERT: C 380 MET cc_start: 0.7400 (mtm) cc_final: 0.7086 (mmp) REVERT: C 393 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5240 (mt) REVERT: C 512 ARG cc_start: 0.7457 (tpt90) cc_final: 0.7119 (tpp80) REVERT: C 551 ASN cc_start: 0.8351 (t0) cc_final: 0.8001 (t0) REVERT: C 728 MET cc_start: 0.7202 (mmt) cc_final: 0.6826 (mmp) REVERT: C 756 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6425 (mt-10) REVERT: C 760 LEU cc_start: 0.7746 (mp) cc_final: 0.7383 (mp) REVERT: D 66 MET cc_start: 0.7945 (mmm) cc_final: 0.7720 (mmm) REVERT: D 79 GLU cc_start: 0.7972 (tt0) cc_final: 0.6916 (mm-30) REVERT: D 222 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7304 (mtm-85) REVERT: D 238 LYS cc_start: 0.7176 (ttpp) cc_final: 0.6833 (ttmm) REVERT: D 257 ASP cc_start: 0.7992 (m-30) cc_final: 0.7757 (m-30) REVERT: D 343 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7106 (ttm) REVERT: D 361 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7580 (tttt) REVERT: D 380 MET cc_start: 0.7434 (mtm) cc_final: 0.7123 (mmp) REVERT: D 393 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5291 (mt) REVERT: D 510 LEU cc_start: 0.7040 (mt) cc_final: 0.6569 (tt) REVERT: D 512 ARG cc_start: 0.7452 (tpt90) cc_final: 0.7114 (tpp80) REVERT: D 551 ASN cc_start: 0.8391 (t0) cc_final: 0.8062 (t0) REVERT: D 728 MET cc_start: 0.7206 (mmt) cc_final: 0.6827 (mmp) REVERT: D 756 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6436 (mt-10) REVERT: D 760 LEU cc_start: 0.7675 (mp) cc_final: 0.7314 (mp) outliers start: 48 outliers final: 14 residues processed: 341 average time/residue: 1.3210 time to fit residues: 514.5548 Evaluate side-chains 307 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 283 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP 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 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 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 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.0770 chunk 74 optimal weight: 0.0060 chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 192 optimal weight: 0.1980 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN B 711 GLN C 711 GLN D 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22976 Z= 0.127 Angle : 0.431 7.392 31052 Z= 0.216 Chirality : 0.034 0.148 3468 Planarity : 0.003 0.043 3812 Dihedral : 12.274 178.338 3612 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.01 % Allowed : 14.22 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.16), residues: 2628 helix: 2.58 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 315 HIS 0.003 0.001 HIS B 92 PHE 0.016 0.001 PHE A 520 TYR 0.010 0.001 TYR D 348 ARG 0.003 0.000 ARG C 191 *********************** 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 362 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 314 time to evaluate : 2.972 Fit side-chains REVERT: A 66 MET cc_start: 0.7888 (mmm) cc_final: 0.7627 (mmm) REVERT: A 79 GLU cc_start: 0.8029 (tt0) cc_final: 0.6979 (mm-30) REVERT: A 167 THR cc_start: 0.8233 (p) cc_final: 0.8031 (m) REVERT: A 170 ARG cc_start: 0.7809 (ttm170) cc_final: 0.6505 (pmt170) REVERT: A 222 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7438 (mtm-85) REVERT: A 257 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: A 361 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7566 (tttt) REVERT: A 380 MET cc_start: 0.7456 (mtm) cc_final: 0.7160 (mmp) REVERT: A 393 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5377 (mt) REVERT: A 512 ARG cc_start: 0.7558 (tpt90) cc_final: 0.7180 (tpp80) REVERT: A 516 ASP cc_start: 0.6721 (m-30) cc_final: 0.6483 (m-30) REVERT: A 551 ASN cc_start: 0.8272 (t0) cc_final: 0.7928 (t0) REVERT: A 728 MET cc_start: 0.7238 (mmt) cc_final: 0.6795 (mmp) REVERT: A 756 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6506 (mt-10) REVERT: B 79 GLU cc_start: 0.7947 (tt0) cc_final: 0.6884 (mm-30) REVERT: B 170 ARG cc_start: 0.7812 (ttm170) cc_final: 0.6509 (pmt170) REVERT: B 222 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7446 (mtm-85) REVERT: B 257 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: B 380 MET cc_start: 0.7457 (mtm) cc_final: 0.7163 (mmp) REVERT: B 393 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5390 (mt) REVERT: B 512 ARG cc_start: 0.7558 (tpt90) cc_final: 0.7197 (tpp80) REVERT: B 551 ASN cc_start: 0.8323 (t0) cc_final: 0.8053 (t0) REVERT: B 552 ASN cc_start: 0.7866 (m-40) cc_final: 0.7666 (t0) REVERT: B 570 GLU cc_start: 0.8373 (tp30) cc_final: 0.8079 (mm-30) REVERT: B 728 MET cc_start: 0.7236 (mmt) cc_final: 0.6797 (mmp) REVERT: B 756 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6500 (mt-10) REVERT: C 66 MET cc_start: 0.7937 (mmm) cc_final: 0.7626 (mmm) REVERT: C 79 GLU cc_start: 0.8033 (tt0) cc_final: 0.6942 (mm-30) REVERT: C 167 THR cc_start: 0.8229 (p) cc_final: 0.8023 (m) REVERT: C 170 ARG cc_start: 0.7816 (ttm170) cc_final: 0.6516 (pmt170) REVERT: C 222 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7443 (mtm-85) REVERT: C 257 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: C 361 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7692 (tttt) REVERT: C 380 MET cc_start: 0.7458 (mtm) cc_final: 0.7166 (mmp) REVERT: C 393 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5365 (mt) REVERT: C 512 ARG cc_start: 0.7565 (tpt90) cc_final: 0.7199 (tpp80) REVERT: C 551 ASN cc_start: 0.8324 (t0) cc_final: 0.7976 (t0) REVERT: C 552 ASN cc_start: 0.7876 (m-40) cc_final: 0.7662 (t0) REVERT: C 728 MET cc_start: 0.7238 (mmt) cc_final: 0.6801 (mmp) REVERT: C 756 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6381 (mt-10) REVERT: C 760 LEU cc_start: 0.7622 (mp) cc_final: 0.7269 (mp) REVERT: D 66 MET cc_start: 0.7970 (mmm) cc_final: 0.7657 (mmm) REVERT: D 79 GLU cc_start: 0.7944 (tt0) cc_final: 0.6879 (mm-30) REVERT: D 167 THR cc_start: 0.8231 (p) cc_final: 0.8028 (m) REVERT: D 170 ARG cc_start: 0.7814 (ttm170) cc_final: 0.6513 (pmt170) REVERT: D 222 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7444 (mtm-85) REVERT: D 257 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: D 361 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7626 (tttt) REVERT: D 380 MET cc_start: 0.7457 (mtm) cc_final: 0.7161 (mmp) REVERT: D 393 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5377 (mt) REVERT: D 512 ARG cc_start: 0.7561 (tpt90) cc_final: 0.7197 (tpp80) REVERT: D 551 ASN cc_start: 0.8322 (t0) cc_final: 0.7976 (t0) REVERT: D 728 MET cc_start: 0.7240 (mmt) cc_final: 0.6802 (mmp) REVERT: D 756 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6501 (mt-10) outliers start: 48 outliers final: 0 residues processed: 340 average time/residue: 1.3002 time to fit residues: 505.1335 Evaluate side-chains 290 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 279 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 B residue 257 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 711 GLN B 533 ASN B 711 GLN C 533 ASN C 711 GLN D 533 ASN D 552 ASN D 711 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22976 Z= 0.181 Angle : 0.442 6.172 31052 Z= 0.226 Chirality : 0.035 0.151 3468 Planarity : 0.003 0.045 3812 Dihedral : 11.669 179.720 3612 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.81 % Allowed : 13.80 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.16), residues: 2628 helix: 2.52 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.21 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 315 HIS 0.002 0.001 HIS B 92 PHE 0.016 0.001 PHE D 341 TYR 0.015 0.001 TYR A 524 ARG 0.003 0.000 ARG D 175 *********************** 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 364 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 297 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7932 (tt0) cc_final: 0.6870 (mm-30) REVERT: A 167 THR cc_start: 0.8233 (p) cc_final: 0.8022 (m) REVERT: A 222 ARG cc_start: 0.7866 (ptp-170) cc_final: 0.7443 (mtm-85) REVERT: A 238 LYS cc_start: 0.7125 (ttpp) cc_final: 0.6791 (ttmm) REVERT: A 257 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: A 331 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6820 (tm) REVERT: A 361 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7556 (tttt) REVERT: A 380 MET cc_start: 0.7668 (mtm) cc_final: 0.7236 (mmp) REVERT: A 382 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7420 (mp) REVERT: A 393 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5310 (mt) REVERT: A 429 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: A 512 ARG cc_start: 0.7543 (tpt90) cc_final: 0.7166 (tpp80) REVERT: A 516 ASP cc_start: 0.6500 (m-30) cc_final: 0.6259 (m-30) REVERT: A 551 ASN cc_start: 0.8348 (t0) cc_final: 0.8021 (t0) REVERT: A 756 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6404 (mt-10) REVERT: B 17 ARG cc_start: 0.6247 (mtt90) cc_final: 0.5529 (mmp80) REVERT: B 79 GLU cc_start: 0.7876 (tt0) cc_final: 0.6901 (mm-30) REVERT: B 222 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7442 (mtm-85) REVERT: B 238 LYS cc_start: 0.7126 (ttpp) cc_final: 0.6793 (ttmm) REVERT: B 257 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: B 331 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6729 (tm) REVERT: B 380 MET cc_start: 0.7665 (mtm) cc_final: 0.7238 (mmp) REVERT: B 382 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7414 (mp) REVERT: B 393 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5309 (mt) REVERT: B 512 ARG cc_start: 0.7534 (tpt90) cc_final: 0.7175 (tpp80) REVERT: B 551 ASN cc_start: 0.8410 (t0) cc_final: 0.8144 (t0) REVERT: B 552 ASN cc_start: 0.7935 (m-40) cc_final: 0.7691 (t0) REVERT: B 570 GLU cc_start: 0.8416 (tp30) cc_final: 0.8095 (mm-30) REVERT: B 756 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6477 (mt-10) REVERT: C 66 MET cc_start: 0.7944 (mmm) cc_final: 0.7684 (mmm) REVERT: C 79 GLU cc_start: 0.7928 (tt0) cc_final: 0.6865 (mm-30) REVERT: C 167 THR cc_start: 0.8314 (p) cc_final: 0.8052 (m) REVERT: C 222 ARG cc_start: 0.7868 (ptp-170) cc_final: 0.7450 (mtm-85) REVERT: C 238 LYS cc_start: 0.7127 (ttpp) cc_final: 0.6793 (ttmm) REVERT: C 257 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: C 331 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6823 (tm) REVERT: C 361 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7726 (tttt) REVERT: C 380 MET cc_start: 0.7668 (mtm) cc_final: 0.7240 (mmp) REVERT: C 382 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 393 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5301 (mt) REVERT: C 422 MET cc_start: 0.7372 (tpp) cc_final: 0.6630 (ttp) REVERT: C 512 ARG cc_start: 0.7520 (tpt90) cc_final: 0.7172 (tpp80) REVERT: C 551 ASN cc_start: 0.8410 (t0) cc_final: 0.8141 (t0) REVERT: C 552 ASN cc_start: 0.7941 (m-40) cc_final: 0.7685 (t0) REVERT: C 756 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6462 (mt-10) REVERT: D 79 GLU cc_start: 0.7933 (tt0) cc_final: 0.6871 (mm-30) REVERT: D 167 THR cc_start: 0.8227 (p) cc_final: 0.8018 (m) REVERT: D 222 ARG cc_start: 0.7867 (ptp-170) cc_final: 0.7448 (mtm-85) REVERT: D 238 LYS cc_start: 0.7127 (ttpp) cc_final: 0.6793 (ttmm) REVERT: D 257 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: D 331 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6767 (tm) REVERT: D 361 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7738 (tttt) REVERT: D 380 MET cc_start: 0.7669 (mtm) cc_final: 0.7237 (mmp) REVERT: D 382 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7411 (mp) REVERT: D 393 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5304 (mt) REVERT: D 422 MET cc_start: 0.7372 (tpp) cc_final: 0.6626 (ttp) REVERT: D 512 ARG cc_start: 0.7535 (tpt90) cc_final: 0.7175 (tpp80) REVERT: D 551 ASN cc_start: 0.8445 (t0) cc_final: 0.8091 (t0) REVERT: D 756 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6460 (mt-10) outliers start: 67 outliers final: 14 residues processed: 339 average time/residue: 1.2061 time to fit residues: 473.6751 Evaluate side-chains 317 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 283 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 429 GLU 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 382 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 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 331 LEU Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 552 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22976 Z= 0.304 Angle : 0.521 6.452 31052 Z= 0.264 Chirality : 0.038 0.157 3468 Planarity : 0.004 0.047 3812 Dihedral : 11.901 176.803 3612 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.77 % Allowed : 14.05 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.16), residues: 2628 helix: 2.23 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.09 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 315 HIS 0.003 0.001 HIS A 473 PHE 0.016 0.002 PHE A 341 TYR 0.019 0.002 TYR A 524 ARG 0.003 0.000 ARG A 17 *********************** 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 377 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 311 time to evaluate : 2.573 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7918 (tt0) cc_final: 0.6886 (mm-30) REVERT: A 81 GLU cc_start: 0.6476 (mt-10) cc_final: 0.5986 (tm-30) REVERT: A 222 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7327 (mtm-85) REVERT: A 238 LYS cc_start: 0.7286 (ttpp) cc_final: 0.6968 (ttmm) REVERT: A 257 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: A 331 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6904 (tm) REVERT: A 380 MET cc_start: 0.7480 (mtm) cc_final: 0.7129 (mmp) REVERT: A 393 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5233 (mt) REVERT: A 422 MET cc_start: 0.7367 (tpp) cc_final: 0.6624 (ttp) REVERT: A 512 ARG cc_start: 0.7678 (tpt90) cc_final: 0.7154 (tpp80) REVERT: A 516 ASP cc_start: 0.6731 (m-30) cc_final: 0.6500 (m-30) REVERT: A 529 LEU cc_start: 0.7866 (tp) cc_final: 0.7614 (mt) REVERT: A 551 ASN cc_start: 0.8543 (t0) cc_final: 0.8213 (t0) REVERT: A 619 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: A 728 MET cc_start: 0.7287 (mmt) cc_final: 0.6868 (mmp) REVERT: A 756 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6703 (mt-10) REVERT: B 79 GLU cc_start: 0.7910 (tt0) cc_final: 0.6921 (mm-30) REVERT: B 81 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5894 (tm-30) REVERT: B 222 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7330 (mtm-85) REVERT: B 238 LYS cc_start: 0.7370 (ttpp) cc_final: 0.7054 (ttmm) REVERT: B 257 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: B 331 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6811 (tm) REVERT: B 380 MET cc_start: 0.7477 (mtm) cc_final: 0.7129 (mmp) REVERT: B 393 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5229 (mt) REVERT: B 422 MET cc_start: 0.7324 (tpp) cc_final: 0.6581 (ttp) REVERT: B 512 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7180 (tpp80) REVERT: B 529 LEU cc_start: 0.7866 (tp) cc_final: 0.7619 (mt) REVERT: B 570 GLU cc_start: 0.8414 (tp30) cc_final: 0.8080 (mm-30) REVERT: B 619 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: B 728 MET cc_start: 0.7287 (mmt) cc_final: 0.6704 (mmp) REVERT: B 756 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6697 (mt-10) REVERT: C 79 GLU cc_start: 0.7910 (tt0) cc_final: 0.6907 (mm-30) REVERT: C 81 GLU cc_start: 0.6463 (mt-10) cc_final: 0.6000 (tm-30) REVERT: C 222 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7327 (mtm-85) REVERT: C 238 LYS cc_start: 0.7384 (ttpp) cc_final: 0.7043 (ttmm) REVERT: C 257 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: C 331 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6907 (tm) REVERT: C 380 MET cc_start: 0.7475 (mtm) cc_final: 0.7128 (mmp) REVERT: C 393 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5235 (mt) REVERT: C 422 MET cc_start: 0.7307 (tpp) cc_final: 0.6643 (ttp) REVERT: C 512 ARG cc_start: 0.7688 (tpt90) cc_final: 0.7182 (tpp80) REVERT: C 529 LEU cc_start: 0.7863 (tp) cc_final: 0.7617 (mt) REVERT: C 728 MET cc_start: 0.7287 (mmt) cc_final: 0.6702 (mmp) REVERT: C 756 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6701 (mt-10) REVERT: D 79 GLU cc_start: 0.7912 (tt0) cc_final: 0.6882 (mm-30) REVERT: D 81 GLU cc_start: 0.6478 (mt-10) cc_final: 0.5990 (tm-30) REVERT: D 222 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7327 (mtm-85) REVERT: D 238 LYS cc_start: 0.7361 (ttpp) cc_final: 0.7046 (ttmm) REVERT: D 257 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: D 331 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6908 (tm) REVERT: D 380 MET cc_start: 0.7479 (mtm) cc_final: 0.7148 (mmp) REVERT: D 393 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5223 (mt) REVERT: D 422 MET cc_start: 0.7308 (tpp) cc_final: 0.6642 (ttp) REVERT: D 512 ARG cc_start: 0.7688 (tpt90) cc_final: 0.7182 (tpp80) REVERT: D 529 LEU cc_start: 0.7830 (tp) cc_final: 0.7604 (mt) REVERT: D 728 MET cc_start: 0.7290 (mmt) cc_final: 0.6705 (mmp) REVERT: D 756 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6697 (mt-10) outliers start: 66 outliers final: 20 residues processed: 349 average time/residue: 1.2240 time to fit residues: 492.3570 Evaluate side-chains 323 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 289 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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 356 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 108 VAL 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 619 MET Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 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 85 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 326 HIS A 533 ASN B 309 GLN B 326 HIS B 533 ASN C 326 HIS C 533 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22976 Z= 0.141 Angle : 0.422 6.360 31052 Z= 0.217 Chirality : 0.034 0.150 3468 Planarity : 0.003 0.048 3812 Dihedral : 11.212 179.982 3612 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.85 % Allowed : 16.07 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.16), residues: 2628 helix: 2.52 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.003 0.001 HIS C 271 PHE 0.022 0.001 PHE A 427 TYR 0.010 0.001 TYR C 200 ARG 0.002 0.000 ARG B 191 *********************** 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 327 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 283 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7898 (tt0) cc_final: 0.6916 (mm-30) REVERT: A 81 GLU cc_start: 0.6518 (mt-10) cc_final: 0.5899 (tm-30) REVERT: A 222 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7419 (mtm-85) REVERT: A 257 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: A 331 LEU cc_start: 0.7260 (mt) cc_final: 0.6930 (tm) REVERT: A 361 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7597 (tttt) REVERT: A 380 MET cc_start: 0.7557 (mtm) cc_final: 0.7233 (mmp) REVERT: A 393 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5266 (mt) REVERT: A 422 MET cc_start: 0.7505 (tpp) cc_final: 0.6855 (ttp) REVERT: A 512 ARG cc_start: 0.7723 (tpt90) cc_final: 0.7210 (tpp80) REVERT: A 529 LEU cc_start: 0.7887 (tp) cc_final: 0.7654 (mt) REVERT: A 551 ASN cc_start: 0.8446 (t0) cc_final: 0.8115 (t0) REVERT: A 728 MET cc_start: 0.7242 (mmt) cc_final: 0.6804 (mmp) REVERT: A 756 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6630 (mt-10) REVERT: B 79 GLU cc_start: 0.7896 (tt0) cc_final: 0.6921 (mm-30) REVERT: B 81 GLU cc_start: 0.6507 (mt-10) cc_final: 0.5926 (tm-30) REVERT: B 170 ARG cc_start: 0.7826 (ttm170) cc_final: 0.6510 (pmt170) REVERT: B 222 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7418 (mtm-85) REVERT: B 257 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: B 331 LEU cc_start: 0.7104 (mt) cc_final: 0.6819 (tm) REVERT: B 380 MET cc_start: 0.7554 (mtm) cc_final: 0.7233 (mmp) REVERT: B 393 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5271 (mt) REVERT: B 422 MET cc_start: 0.7395 (tpp) cc_final: 0.6690 (ttp) REVERT: B 512 ARG cc_start: 0.7741 (tpt90) cc_final: 0.7215 (tpp80) REVERT: B 529 LEU cc_start: 0.7887 (tp) cc_final: 0.7662 (mt) REVERT: B 570 GLU cc_start: 0.8349 (tp30) cc_final: 0.8048 (mm-30) REVERT: B 728 MET cc_start: 0.7243 (mmt) cc_final: 0.6804 (mmp) REVERT: B 756 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6630 (mt-10) REVERT: C 79 GLU cc_start: 0.7900 (tt0) cc_final: 0.6904 (mm-30) REVERT: C 81 GLU cc_start: 0.6543 (mt-10) cc_final: 0.5867 (tm-30) REVERT: C 222 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7424 (mtm-85) REVERT: C 257 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: C 331 LEU cc_start: 0.7261 (mt) cc_final: 0.6927 (tm) REVERT: C 380 MET cc_start: 0.7553 (mtm) cc_final: 0.7235 (mmp) REVERT: C 393 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5259 (mt) REVERT: C 422 MET cc_start: 0.7408 (tpp) cc_final: 0.6737 (ttp) REVERT: C 512 ARG cc_start: 0.7742 (tpt90) cc_final: 0.7214 (tpp80) REVERT: C 529 LEU cc_start: 0.7898 (tp) cc_final: 0.7678 (mt) REVERT: C 728 MET cc_start: 0.7242 (mmt) cc_final: 0.6803 (mmp) REVERT: C 756 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6630 (mt-10) REVERT: D 79 GLU cc_start: 0.7898 (tt0) cc_final: 0.6916 (mm-30) REVERT: D 81 GLU cc_start: 0.6524 (mt-10) cc_final: 0.5846 (tm-30) REVERT: D 222 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7417 (mtm-85) REVERT: D 257 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: D 331 LEU cc_start: 0.7262 (mt) cc_final: 0.6929 (tm) REVERT: D 380 MET cc_start: 0.7559 (mtm) cc_final: 0.7233 (mmp) REVERT: D 393 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5258 (mt) REVERT: D 422 MET cc_start: 0.7410 (tpp) cc_final: 0.6736 (ttp) REVERT: D 512 ARG cc_start: 0.7742 (tpt90) cc_final: 0.7216 (tpp80) REVERT: D 529 LEU cc_start: 0.7887 (tp) cc_final: 0.7630 (mt) REVERT: D 728 MET cc_start: 0.7243 (mmt) cc_final: 0.6805 (mmp) REVERT: D 756 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6634 (mt-10) outliers start: 44 outliers final: 13 residues processed: 318 average time/residue: 1.1965 time to fit residues: 439.9963 Evaluate side-chains 293 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 271 time to evaluate : 2.396 ------------------------------------------------------------------------------- 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 382 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 0.0010 chunk 186 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- 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 C 326 HIS C 533 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22976 Z= 0.206 Angle : 0.460 6.213 31052 Z= 0.233 Chirality : 0.035 0.161 3468 Planarity : 0.004 0.048 3812 Dihedral : 11.196 177.128 3612 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.64 % Allowed : 16.07 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.16), residues: 2628 helix: 2.45 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.02 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 315 HIS 0.002 0.001 HIS C 92 PHE 0.021 0.001 PHE A 520 TYR 0.016 0.001 TYR A 524 ARG 0.002 0.000 ARG A 191 *********************** 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 318 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 279 time to evaluate : 2.665 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7900 (tt0) cc_final: 0.6917 (mm-30) REVERT: A 81 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6054 (tm-30) REVERT: A 222 ARG cc_start: 0.7823 (ptp-170) cc_final: 0.7424 (mtm-85) REVERT: A 257 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: A 331 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6922 (tm) REVERT: A 361 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7607 (tttt) REVERT: A 380 MET cc_start: 0.7541 (mtm) cc_final: 0.7231 (mmp) REVERT: A 393 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5203 (mt) REVERT: A 422 MET cc_start: 0.7469 (tpp) cc_final: 0.6770 (ttp) REVERT: A 512 ARG cc_start: 0.7819 (tpt90) cc_final: 0.7238 (tpp80) REVERT: A 529 LEU cc_start: 0.7850 (tp) cc_final: 0.7617 (mt) REVERT: A 551 ASN cc_start: 0.8379 (t0) cc_final: 0.8069 (t0) REVERT: A 728 MET cc_start: 0.7267 (mmt) cc_final: 0.6800 (mmp) REVERT: A 756 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6617 (mt-10) REVERT: A 758 LEU cc_start: 0.6626 (mt) cc_final: 0.6374 (mt) REVERT: B 79 GLU cc_start: 0.7898 (tt0) cc_final: 0.6918 (mm-30) REVERT: B 81 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6058 (tm-30) REVERT: B 170 ARG cc_start: 0.7784 (ttm170) cc_final: 0.6430 (pmt170) REVERT: B 222 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.7431 (mtm-85) REVERT: B 257 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: B 331 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6813 (tm) REVERT: B 380 MET cc_start: 0.7539 (mtm) cc_final: 0.7232 (mmp) REVERT: B 393 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5236 (mt) REVERT: B 422 MET cc_start: 0.7392 (tpp) cc_final: 0.6668 (ttp) REVERT: B 512 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7226 (tpp80) REVERT: B 529 LEU cc_start: 0.7904 (tp) cc_final: 0.7680 (mt) REVERT: B 570 GLU cc_start: 0.8367 (tp30) cc_final: 0.8026 (mm-30) REVERT: B 593 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8033 (ttm110) REVERT: B 728 MET cc_start: 0.7268 (mmt) cc_final: 0.6801 (mmp) REVERT: B 756 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 758 LEU cc_start: 0.6616 (mt) cc_final: 0.6354 (mt) REVERT: C 79 GLU cc_start: 0.7896 (tt0) cc_final: 0.6908 (mm-30) REVERT: C 81 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6052 (tm-30) REVERT: C 222 ARG cc_start: 0.7825 (ptp-170) cc_final: 0.7431 (mtm-85) REVERT: C 257 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: C 331 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6919 (tm) REVERT: C 380 MET cc_start: 0.7538 (mtm) cc_final: 0.7238 (mmp) REVERT: C 393 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5224 (mt) REVERT: C 422 MET cc_start: 0.7394 (tpp) cc_final: 0.6731 (ttp) REVERT: C 512 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7227 (tpp80) REVERT: C 529 LEU cc_start: 0.7848 (tp) cc_final: 0.7618 (mt) REVERT: C 728 MET cc_start: 0.7268 (mmt) cc_final: 0.6800 (mmp) REVERT: C 756 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6619 (mt-10) REVERT: C 758 LEU cc_start: 0.6639 (mt) cc_final: 0.6352 (mt) REVERT: D 79 GLU cc_start: 0.7902 (tt0) cc_final: 0.6915 (mm-30) REVERT: D 81 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6047 (tm-30) REVERT: D 222 ARG cc_start: 0.7823 (ptp-170) cc_final: 0.7429 (mtm-85) REVERT: D 257 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 331 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6921 (tm) REVERT: D 380 MET cc_start: 0.7541 (mtm) cc_final: 0.7230 (mmp) REVERT: D 393 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5162 (mt) REVERT: D 422 MET cc_start: 0.7392 (tpp) cc_final: 0.6729 (ttp) REVERT: D 512 ARG cc_start: 0.7820 (tpt90) cc_final: 0.7227 (tpp80) REVERT: D 529 LEU cc_start: 0.7853 (tp) cc_final: 0.7593 (mt) REVERT: D 728 MET cc_start: 0.7269 (mmt) cc_final: 0.6802 (mmp) REVERT: D 756 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6623 (mt-10) REVERT: D 758 LEU cc_start: 0.6627 (mt) cc_final: 0.6368 (mt) outliers start: 39 outliers final: 13 residues processed: 302 average time/residue: 1.1952 time to fit residues: 417.4769 Evaluate side-chains 305 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 278 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 C 326 HIS C 533 ASN C 742 ASN D 326 HIS D 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22976 Z= 0.138 Angle : 0.417 6.399 31052 Z= 0.213 Chirality : 0.034 0.158 3468 Planarity : 0.003 0.048 3812 Dihedral : 10.814 179.503 3612 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.68 % Allowed : 16.65 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.16), residues: 2628 helix: 2.61 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 315 HIS 0.002 0.000 HIS B 92 PHE 0.017 0.001 PHE A 427 TYR 0.011 0.001 TYR A 524 ARG 0.002 0.000 ARG A 593 *********************** 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 319 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 2.731 Fit side-chains REVERT: A 79 GLU cc_start: 0.7904 (tt0) cc_final: 0.6925 (mm-30) REVERT: A 81 GLU cc_start: 0.6647 (mt-10) cc_final: 0.5969 (tm-30) REVERT: A 170 ARG cc_start: 0.7813 (ttm170) cc_final: 0.6504 (pmt170) REVERT: A 222 ARG cc_start: 0.7754 (ptp-170) cc_final: 0.7395 (mtm-85) REVERT: A 257 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: A 331 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6801 (tm) REVERT: A 361 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7603 (tttt) REVERT: A 380 MET cc_start: 0.7512 (mtm) cc_final: 0.7241 (mmp) REVERT: A 393 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5212 (mt) REVERT: A 422 MET cc_start: 0.7432 (tpp) cc_final: 0.6754 (ttp) REVERT: A 512 ARG cc_start: 0.7867 (tpt90) cc_final: 0.7244 (tpp80) REVERT: A 529 LEU cc_start: 0.7863 (tp) cc_final: 0.7644 (mt) REVERT: A 551 ASN cc_start: 0.8315 (t0) cc_final: 0.7990 (t0) REVERT: A 728 MET cc_start: 0.7228 (mmt) cc_final: 0.6738 (mmp) REVERT: A 756 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 758 LEU cc_start: 0.6657 (mt) cc_final: 0.6422 (mt) REVERT: B 79 GLU cc_start: 0.7900 (tt0) cc_final: 0.6925 (mm-30) REVERT: B 81 GLU cc_start: 0.6682 (mt-10) cc_final: 0.5992 (tm-30) REVERT: B 170 ARG cc_start: 0.7784 (ttm170) cc_final: 0.6413 (pmt170) REVERT: B 222 ARG cc_start: 0.7752 (ptp-170) cc_final: 0.7395 (mtm-85) REVERT: B 257 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: B 331 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6799 (tm) REVERT: B 380 MET cc_start: 0.7510 (mtm) cc_final: 0.7242 (mmp) REVERT: B 393 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5219 (mt) REVERT: B 422 MET cc_start: 0.7409 (tpp) cc_final: 0.6707 (ttp) REVERT: B 512 ARG cc_start: 0.7842 (tpt90) cc_final: 0.7242 (tpp80) REVERT: B 529 LEU cc_start: 0.7891 (tp) cc_final: 0.7669 (mt) REVERT: B 570 GLU cc_start: 0.8342 (tp30) cc_final: 0.8044 (mm-30) REVERT: B 728 MET cc_start: 0.7230 (mmt) cc_final: 0.6741 (mmp) REVERT: B 756 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6628 (mt-10) REVERT: B 758 LEU cc_start: 0.6580 (mt) cc_final: 0.6347 (mt) REVERT: C 79 GLU cc_start: 0.7905 (tt0) cc_final: 0.6926 (mm-30) REVERT: C 81 GLU cc_start: 0.6636 (mt-10) cc_final: 0.5965 (tm-30) REVERT: C 170 ARG cc_start: 0.7817 (ttm170) cc_final: 0.6508 (pmt170) REVERT: C 222 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7396 (mtm-85) REVERT: C 257 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: C 331 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6737 (tm) REVERT: C 380 MET cc_start: 0.7475 (mtm) cc_final: 0.7245 (mmp) REVERT: C 382 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7261 (mp) REVERT: C 393 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5191 (mt) REVERT: C 422 MET cc_start: 0.7388 (tpp) cc_final: 0.6772 (ttp) REVERT: C 512 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7242 (tpp80) REVERT: C 529 LEU cc_start: 0.7886 (tp) cc_final: 0.7660 (mt) REVERT: C 728 MET cc_start: 0.7258 (mmt) cc_final: 0.6733 (mmp) REVERT: C 756 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6614 (mt-10) REVERT: C 758 LEU cc_start: 0.6587 (mt) cc_final: 0.6332 (mt) REVERT: D 79 GLU cc_start: 0.7905 (tt0) cc_final: 0.6923 (mm-30) REVERT: D 81 GLU cc_start: 0.6646 (mt-10) cc_final: 0.5969 (tm-30) REVERT: D 170 ARG cc_start: 0.7810 (ttm170) cc_final: 0.6514 (pmt170) REVERT: D 222 ARG cc_start: 0.7750 (ptp-170) cc_final: 0.7394 (mtm-85) REVERT: D 257 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: D 331 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6741 (tm) REVERT: D 380 MET cc_start: 0.7513 (mtm) cc_final: 0.7241 (mmp) REVERT: D 393 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5180 (mt) REVERT: D 422 MET cc_start: 0.7386 (tpp) cc_final: 0.6770 (ttp) REVERT: D 512 ARG cc_start: 0.7839 (tpt90) cc_final: 0.7249 (tpp80) REVERT: D 529 LEU cc_start: 0.7888 (tp) cc_final: 0.7646 (mt) REVERT: D 728 MET cc_start: 0.7231 (mmt) cc_final: 0.6741 (mmp) REVERT: D 756 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6615 (mt-10) REVERT: D 758 LEU cc_start: 0.6691 (mt) cc_final: 0.6446 (mt) outliers start: 40 outliers final: 12 residues processed: 303 average time/residue: 1.1933 time to fit residues: 419.3718 Evaluate side-chains 292 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 711 GLN B 326 HIS B 711 GLN C 326 HIS C 533 ASN C 711 GLN D 326 HIS D 533 ASN D 711 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22976 Z= 0.200 Angle : 0.457 7.335 31052 Z= 0.230 Chirality : 0.035 0.165 3468 Planarity : 0.004 0.048 3812 Dihedral : 10.876 177.613 3612 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.38 % Allowed : 17.03 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.16), residues: 2628 helix: 2.49 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.002 0.001 HIS B 92 PHE 0.024 0.001 PHE A 520 TYR 0.015 0.001 TYR C 524 ARG 0.002 0.000 ARG C 593 *********************** 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 311 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 278 time to evaluate : 2.751 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7912 (tt0) cc_final: 0.6910 (mm-30) REVERT: A 81 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6063 (tm-30) REVERT: A 170 ARG cc_start: 0.7822 (ttm170) cc_final: 0.6506 (pmt170) REVERT: A 222 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7414 (mtm-85) REVERT: A 257 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: A 331 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6740 (tm) REVERT: A 361 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7666 (tttt) REVERT: A 380 MET cc_start: 0.7531 (mtm) cc_final: 0.7241 (mmp) REVERT: A 393 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5244 (mt) REVERT: A 422 MET cc_start: 0.7403 (tpp) cc_final: 0.6692 (ttp) REVERT: A 512 ARG cc_start: 0.7897 (tpt90) cc_final: 0.7262 (tpp80) REVERT: A 529 LEU cc_start: 0.7905 (tp) cc_final: 0.7682 (mt) REVERT: A 551 ASN cc_start: 0.8350 (t0) cc_final: 0.8034 (t0) REVERT: A 728 MET cc_start: 0.7272 (mmt) cc_final: 0.6783 (mmp) REVERT: A 756 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6552 (mt-10) REVERT: A 758 LEU cc_start: 0.6663 (mt) cc_final: 0.6407 (mt) REVERT: B 79 GLU cc_start: 0.7896 (tt0) cc_final: 0.6923 (mm-30) REVERT: B 81 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6057 (tm-30) REVERT: B 170 ARG cc_start: 0.7771 (ttm170) cc_final: 0.6425 (pmt170) REVERT: B 222 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7414 (mtm-85) REVERT: B 257 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: B 331 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6820 (tm) REVERT: B 380 MET cc_start: 0.7511 (mtm) cc_final: 0.7220 (mmp) REVERT: B 393 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5300 (mt) REVERT: B 422 MET cc_start: 0.7334 (tpp) cc_final: 0.6599 (ttp) REVERT: B 512 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7281 (tpp80) REVERT: B 529 LEU cc_start: 0.7903 (tp) cc_final: 0.7686 (mt) REVERT: B 570 GLU cc_start: 0.8367 (tp30) cc_final: 0.8024 (mm-30) REVERT: B 728 MET cc_start: 0.7274 (mmt) cc_final: 0.6786 (mmp) REVERT: B 756 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 758 LEU cc_start: 0.6675 (mt) cc_final: 0.6446 (mt) REVERT: C 79 GLU cc_start: 0.7906 (tt0) cc_final: 0.6937 (mm-30) REVERT: C 81 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6058 (tm-30) REVERT: C 222 ARG cc_start: 0.7782 (ptp-170) cc_final: 0.7414 (mtm-85) REVERT: C 257 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: C 331 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6736 (tm) REVERT: C 380 MET cc_start: 0.7507 (mtm) cc_final: 0.7227 (mmp) REVERT: C 393 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5259 (mt) REVERT: C 422 MET cc_start: 0.7406 (tpp) cc_final: 0.6756 (ttp) REVERT: C 512 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7265 (tpp80) REVERT: C 529 LEU cc_start: 0.7902 (tp) cc_final: 0.7683 (mt) REVERT: C 728 MET cc_start: 0.7272 (mmt) cc_final: 0.6784 (mmp) REVERT: C 756 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6619 (mt-10) REVERT: C 758 LEU cc_start: 0.6704 (mt) cc_final: 0.6458 (mt) REVERT: D 79 GLU cc_start: 0.7915 (tt0) cc_final: 0.6909 (mm-30) REVERT: D 81 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6064 (tm-30) REVERT: D 170 ARG cc_start: 0.7822 (ttm170) cc_final: 0.6521 (pmt170) REVERT: D 222 ARG cc_start: 0.7782 (ptp-170) cc_final: 0.7413 (mtm-85) REVERT: D 257 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: D 331 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6740 (tm) REVERT: D 380 MET cc_start: 0.7513 (mtm) cc_final: 0.7219 (mmp) REVERT: D 393 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5254 (mt) REVERT: D 422 MET cc_start: 0.7406 (tpp) cc_final: 0.6755 (ttp) REVERT: D 512 ARG cc_start: 0.7896 (tpt90) cc_final: 0.7269 (tpp80) REVERT: D 529 LEU cc_start: 0.7905 (tp) cc_final: 0.7655 (mt) REVERT: D 728 MET cc_start: 0.7268 (mmt) cc_final: 0.6771 (mmp) REVERT: D 756 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6616 (mt-10) REVERT: D 758 LEU cc_start: 0.6669 (mt) cc_final: 0.6416 (mt) outliers start: 33 outliers final: 14 residues processed: 302 average time/residue: 1.2444 time to fit residues: 434.7845 Evaluate side-chains 303 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 276 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 174 optimal weight: 0.0060 chunk 263 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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 711 GLN A 742 ASN B 326 HIS B 711 GLN B 742 ASN C 326 HIS C 533 ASN C 711 GLN D 326 HIS D 533 ASN D 711 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22976 Z= 0.187 Angle : 0.452 7.930 31052 Z= 0.228 Chirality : 0.035 0.162 3468 Planarity : 0.003 0.049 3812 Dihedral : 10.847 177.466 3612 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.26 % Allowed : 17.41 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.16), residues: 2628 helix: 2.50 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.01 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 315 HIS 0.002 0.000 HIS B 92 PHE 0.017 0.001 PHE D 341 TYR 0.013 0.001 TYR C 524 ARG 0.002 0.000 ARG C 593 ********************** 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 306 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 2.542 Fit side-chains REVERT: A 79 GLU cc_start: 0.7907 (tt0) cc_final: 0.6908 (mm-30) REVERT: A 81 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6063 (tm-30) REVERT: A 170 ARG cc_start: 0.7818 (ttm170) cc_final: 0.6503 (pmt170) REVERT: A 222 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7411 (mtm-85) REVERT: A 257 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: A 331 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6740 (tm) REVERT: A 380 MET cc_start: 0.7479 (mtm) cc_final: 0.7224 (mmp) REVERT: A 393 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5229 (mt) REVERT: A 422 MET cc_start: 0.7407 (tpp) cc_final: 0.6694 (ttp) REVERT: A 512 ARG cc_start: 0.7907 (tpt90) cc_final: 0.7262 (tpp80) REVERT: A 529 LEU cc_start: 0.7902 (tp) cc_final: 0.7684 (mt) REVERT: A 551 ASN cc_start: 0.8328 (t0) cc_final: 0.7998 (t0) REVERT: A 728 MET cc_start: 0.7280 (mmt) cc_final: 0.6789 (mmp) REVERT: A 756 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6647 (mt-10) REVERT: A 758 LEU cc_start: 0.6591 (mt) cc_final: 0.6355 (mt) REVERT: B 79 GLU cc_start: 0.7893 (tt0) cc_final: 0.6924 (mm-30) REVERT: B 81 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6058 (tm-30) REVERT: B 170 ARG cc_start: 0.7765 (ttm170) cc_final: 0.6419 (pmt170) REVERT: B 222 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7412 (mtm-85) REVERT: B 257 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: B 331 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6760 (tm) REVERT: B 380 MET cc_start: 0.7477 (mtm) cc_final: 0.7223 (mmp) REVERT: B 393 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5228 (mt) REVERT: B 422 MET cc_start: 0.7328 (tpp) cc_final: 0.6597 (ttp) REVERT: B 512 ARG cc_start: 0.7910 (tpt90) cc_final: 0.7261 (tpp80) REVERT: B 529 LEU cc_start: 0.7903 (tp) cc_final: 0.7690 (mt) REVERT: B 570 GLU cc_start: 0.8354 (tp30) cc_final: 0.8060 (mm-30) REVERT: B 728 MET cc_start: 0.7309 (mmt) cc_final: 0.6789 (mmp) REVERT: B 756 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6683 (mt-10) REVERT: B 758 LEU cc_start: 0.6661 (mt) cc_final: 0.6424 (mt) REVERT: C 79 GLU cc_start: 0.7901 (tt0) cc_final: 0.6935 (mm-30) REVERT: C 81 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6057 (tm-30) REVERT: C 170 ARG cc_start: 0.7784 (ttm170) cc_final: 0.6477 (pmt170) REVERT: C 222 ARG cc_start: 0.7780 (ptp-170) cc_final: 0.7411 (mtm-85) REVERT: C 257 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: C 331 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6736 (tm) REVERT: C 380 MET cc_start: 0.7474 (mtm) cc_final: 0.7232 (mmp) REVERT: C 393 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5249 (mt) REVERT: C 422 MET cc_start: 0.7351 (tpp) cc_final: 0.6706 (ttp) REVERT: C 512 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7262 (tpp80) REVERT: C 529 LEU cc_start: 0.7901 (tp) cc_final: 0.7685 (mt) REVERT: C 728 MET cc_start: 0.7311 (mmt) cc_final: 0.6792 (mmp) REVERT: C 756 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6643 (mt-10) REVERT: C 758 LEU cc_start: 0.6688 (mt) cc_final: 0.6429 (mt) REVERT: D 79 GLU cc_start: 0.7899 (tt0) cc_final: 0.6934 (mm-30) REVERT: D 81 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6063 (tm-30) REVERT: D 170 ARG cc_start: 0.7778 (ttm170) cc_final: 0.6453 (pmt170) REVERT: D 222 ARG cc_start: 0.7780 (ptp-170) cc_final: 0.7411 (mtm-85) REVERT: D 257 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: D 331 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6740 (tm) REVERT: D 380 MET cc_start: 0.7482 (mtm) cc_final: 0.7225 (mmp) REVERT: D 393 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5245 (mt) REVERT: D 422 MET cc_start: 0.7402 (tpp) cc_final: 0.6752 (ttp) REVERT: D 512 ARG cc_start: 0.7910 (tpt90) cc_final: 0.7262 (tpp80) REVERT: D 529 LEU cc_start: 0.7904 (tp) cc_final: 0.7657 (mt) REVERT: D 728 MET cc_start: 0.7305 (mmt) cc_final: 0.6776 (mmp) REVERT: D 756 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6606 (mt-10) REVERT: D 758 LEU cc_start: 0.6591 (mt) cc_final: 0.6340 (mt) outliers start: 30 outliers final: 14 residues processed: 299 average time/residue: 1.2902 time to fit residues: 444.7367 Evaluate side-chains 304 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 2.731 ------------------------------------------------------------------------------- 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 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 717 ILE Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 711 GLN B 326 HIS B 711 GLN C 326 HIS C 533 ASN C 711 GLN D 326 HIS D 533 ASN D 711 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112633 restraints weight = 23922.045| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.17 r_work: 0.3202 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22976 Z= 0.253 Angle : 0.491 8.494 31052 Z= 0.247 Chirality : 0.036 0.170 3468 Planarity : 0.004 0.048 3812 Dihedral : 11.158 175.360 3612 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.59 % Allowed : 16.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.16), residues: 2628 helix: 2.35 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.09 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.002 0.001 HIS A 473 PHE 0.021 0.002 PHE A 520 TYR 0.018 0.001 TYR A 524 ARG 0.002 0.000 ARG C 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8212.15 seconds wall clock time: 144 minutes 16.63 seconds (8656.63 seconds total)