Starting phenix.real_space_refine on Fri Jun 20 07:47:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d4p_30575/06_2025/7d4p_30575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d4p_30575/06_2025/7d4p_30575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d4p_30575/06_2025/7d4p_30575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d4p_30575/06_2025/7d4p_30575.map" model { file = "/net/cci-nas-00/data/ceres_data/7d4p_30575/06_2025/7d4p_30575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d4p_30575/06_2025/7d4p_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.51, per 1000 atoms: 0.65 Number of scatterers: 22472 At special positions: 0 Unit cell: (113.905, 113.905, 136.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 Cl 4 17.00 S 116 16.00 P 8 15.00 O 3988 8.00 N 3592 7.00 C 14756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.04 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.04 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 2.7 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: 2.52 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: 7.36 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3520 1.29 - 1.42: 5964 1.42 - 1.56: 13284 1.56 - 1.69: 16 1.69 - 1.82: 192 Bond restraints: 22976 Sorted by residual: bond pdb=" C12 YZY D 807 " pdb=" C13 YZY D 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY A 807 " pdb=" C13 YZY A 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY C 807 " pdb=" C13 YZY C 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY B 807 " pdb=" C13 YZY B 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C29 YZY A 807 " pdb=" C30 YZY A 807 " ideal model delta sigma weight residual 1.497 1.325 0.172 2.00e-02 2.50e+03 7.44e+01 ... (remaining 22971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 30840 3.86 - 7.72: 148 7.72 - 11.57: 48 11.57 - 15.43: 12 15.43 - 19.29: 4 Bond angle restraints: 31052 Sorted by residual: angle pdb=" C27 YZY C 807 " pdb=" C28 YZY C 807 " pdb=" C29 YZY C 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY A 807 " pdb=" C28 YZY A 807 " pdb=" C29 YZY A 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY D 807 " pdb=" C28 YZY D 807 " pdb=" C29 YZY D 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY B 807 " pdb=" C28 YZY B 807 " pdb=" C29 YZY B 807 " ideal model delta sigma weight residual 128.13 108.85 19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C21 YZY C 807 " pdb=" C20 YZY C 807 " pdb=" O4 YZY C 807 " ideal model delta sigma weight residual 111.77 126.94 -15.17 3.00e+00 1.11e-01 2.56e+01 ... (remaining 31047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.83: 13696 32.83 - 65.67: 268 65.67 - 98.50: 44 98.50 - 131.34: 4 131.34 - 164.17: 8 Dihedral angle restraints: 14020 sinusoidal: 6104 harmonic: 7916 Sorted by residual: dihedral pdb=" C5 YZY D 807 " pdb=" C3 YZY D 807 " pdb=" C4 YZY D 807 " pdb=" O2 YZY D 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.57 164.17 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY B 807 " pdb=" C3 YZY B 807 " pdb=" C4 YZY B 807 " pdb=" O2 YZY B 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.61 164.13 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY A 807 " pdb=" C3 YZY A 807 " pdb=" C4 YZY A 807 " pdb=" O2 YZY A 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.61 164.13 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 14017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2866 0.045 - 0.090: 514 0.090 - 0.134: 72 0.134 - 0.179: 8 0.179 - 0.224: 8 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CBI Y01 A 804 " pdb=" CAU Y01 A 804 " pdb=" CBE Y01 A 804 " pdb=" CBG Y01 A 804 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CBI Y01 B 804 " pdb=" CAU Y01 B 804 " pdb=" CBE Y01 B 804 " pdb=" CBG Y01 B 804 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CBI Y01 C 804 " pdb=" CAU Y01 C 804 " pdb=" CBE Y01 C 804 " pdb=" CBG Y01 C 804 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3465 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 442 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C MET C 442 " 0.037 2.00e-02 2.50e+03 pdb=" O MET C 442 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 443 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 441 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ALA B 441 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA B 441 " 0.014 2.00e-02 2.50e+03 pdb=" N MET B 442 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ALA C 441 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA C 441 " -0.014 2.00e-02 2.50e+03 pdb=" N MET C 442 " -0.012 2.00e-02 2.50e+03 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5178 2.79 - 3.32: 22306 3.32 - 3.85: 37950 3.85 - 4.37: 44644 4.37 - 4.90: 76924 Nonbonded interactions: 187002 Sorted by model distance: nonbonded pdb=" OAH Y01 D 804 " pdb=" OAW Y01 D 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 A 804 " pdb=" OAW Y01 A 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 C 804 " pdb=" OAW Y01 C 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 B 804 " pdb=" OAW Y01 B 804 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.290 3.040 ... (remaining 186997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.230 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 58.070 Find NCS groups from input model: 0.500 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: 0.000 Load rotamer database and sin/cos tables:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.215 22996 Z= 0.354 Angle : 0.798 19.289 31072 Z= 0.333 Chirality : 0.036 0.224 3468 Planarity : 0.004 0.032 3812 Dihedral : 13.898 164.170 8856 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.62 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 Details of bonding type rmsd hydrogen bonds : bond 0.10950 ( 1484) hydrogen bonds : angle 5.06670 ( 4344) metal coordination : bond 0.01136 ( 16) metal coordination : angle 1.33825 ( 12) SS BOND : bond 0.00508 ( 4) SS BOND : angle 0.76098 ( 8) covalent geometry : bond 0.00698 (22976) covalent geometry : angle 0.79763 (31052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 495 time to evaluate : 2.988 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: 1.4406 time to fit residues: 831.6390 Evaluate side-chains 327 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 320 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 573 GLN A 711 GLN B 247 GLN B 573 GLN B 711 GLN C 247 GLN C 573 GLN C 711 GLN D 247 GLN D 533 ASN D 573 GLN D 711 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111857 restraints weight = 24076.240| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.19 r_work: 0.3186 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22996 Z= 0.212 Angle : 0.564 7.112 31072 Z= 0.281 Chirality : 0.039 0.154 3468 Planarity : 0.004 0.040 3812 Dihedral : 13.503 172.690 3618 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.47 % Allowed : 12.84 % Favored : 84.69 % 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: 2.44 (0.16), residues: 2628 helix: 2.12 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 315 HIS 0.003 0.001 HIS B 712 PHE 0.016 0.002 PHE C 341 TYR 0.019 0.002 TYR B 524 ARG 0.004 0.001 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 1484) hydrogen bonds : angle 3.94399 ( 4344) metal coordination : bond 0.00632 ( 16) metal coordination : angle 0.84418 ( 12) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.80663 ( 8) covalent geometry : bond 0.00517 (22976) covalent geometry : angle 0.56368 (31052) *********************** 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 375 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.6988 (pt0) cc_final: 0.6787 (mt0) REVERT: A 79 GLU cc_start: 0.8028 (tt0) cc_final: 0.7019 (mm-30) REVERT: A 222 ARG cc_start: 0.8046 (ptp-170) cc_final: 0.7443 (mtm-85) REVERT: A 238 LYS cc_start: 0.7441 (ttpp) cc_final: 0.7098 (ttmm) REVERT: A 257 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: A 343 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7356 (ttm) REVERT: A 380 MET cc_start: 0.7493 (mtm) cc_final: 0.7198 (mmp) REVERT: A 393 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5397 (mt) REVERT: A 510 LEU cc_start: 0.7062 (mt) cc_final: 0.6626 (tt) REVERT: A 512 ARG cc_start: 0.7547 (tpt90) cc_final: 0.7242 (tpp80) REVERT: A 516 ASP cc_start: 0.6912 (m-30) cc_final: 0.6704 (m-30) REVERT: A 551 ASN cc_start: 0.8566 (t0) cc_final: 0.8255 (t0) REVERT: A 728 MET cc_start: 0.7317 (mmt) cc_final: 0.6951 (mmp) REVERT: A 756 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6626 (mt-10) REVERT: B 79 GLU cc_start: 0.8043 (tt0) cc_final: 0.7026 (mm-30) REVERT: B 222 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7433 (mtm-85) REVERT: B 238 LYS cc_start: 0.7440 (ttpp) cc_final: 0.7099 (ttmm) REVERT: B 257 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: B 343 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7350 (ttm) REVERT: B 380 MET cc_start: 0.7487 (mtm) cc_final: 0.7192 (mmp) REVERT: B 393 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5403 (mt) REVERT: B 510 LEU cc_start: 0.7068 (mt) cc_final: 0.6629 (tt) REVERT: B 512 ARG cc_start: 0.7561 (tpt90) cc_final: 0.7244 (tpp80) REVERT: B 551 ASN cc_start: 0.8503 (t0) cc_final: 0.8192 (t0) REVERT: B 570 GLU cc_start: 0.8608 (tp30) cc_final: 0.8382 (mm-30) REVERT: B 728 MET cc_start: 0.7312 (mmt) cc_final: 0.6949 (mmp) REVERT: B 756 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6662 (mt-10) REVERT: C 79 GLU cc_start: 0.8041 (tt0) cc_final: 0.7037 (mm-30) REVERT: C 222 ARG cc_start: 0.8008 (ptp-170) cc_final: 0.7438 (mtm-85) REVERT: C 238 LYS cc_start: 0.7432 (ttpp) cc_final: 0.7093 (ttmm) REVERT: C 343 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7318 (ttm) REVERT: C 361 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7728 (tttt) REVERT: C 380 MET cc_start: 0.7498 (mtm) cc_final: 0.7208 (mmp) REVERT: C 393 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5396 (mt) REVERT: C 510 LEU cc_start: 0.7080 (mt) cc_final: 0.6638 (tt) REVERT: C 512 ARG cc_start: 0.7568 (tpt90) cc_final: 0.7256 (tpp80) REVERT: C 551 ASN cc_start: 0.8519 (t0) cc_final: 0.8154 (t0) REVERT: C 711 GLN cc_start: 0.7749 (tt0) cc_final: 0.7529 (mt0) REVERT: C 728 MET cc_start: 0.7301 (mmt) cc_final: 0.6939 (mmp) REVERT: C 756 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6706 (mt-10) REVERT: D 21 GLN cc_start: 0.7031 (pt0) cc_final: 0.6824 (mt0) REVERT: D 66 MET cc_start: 0.8059 (mmm) cc_final: 0.7828 (mmm) REVERT: D 79 GLU cc_start: 0.8042 (tt0) cc_final: 0.7038 (mm-30) REVERT: D 222 ARG cc_start: 0.8012 (ptp-170) cc_final: 0.7434 (mtm-85) REVERT: D 238 LYS cc_start: 0.7441 (ttpp) cc_final: 0.7101 (ttmm) REVERT: D 343 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7331 (ttm) REVERT: D 361 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7767 (tttt) REVERT: D 380 MET cc_start: 0.7501 (mtm) cc_final: 0.7207 (mmp) REVERT: D 393 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5403 (mt) REVERT: D 510 LEU cc_start: 0.7091 (mt) cc_final: 0.6649 (tt) REVERT: D 512 ARG cc_start: 0.7555 (tpt90) cc_final: 0.7257 (tpp80) REVERT: D 551 ASN cc_start: 0.8590 (t0) cc_final: 0.8219 (t0) REVERT: D 728 MET cc_start: 0.7305 (mmt) cc_final: 0.6938 (mmp) REVERT: D 756 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6573 (mt-10) REVERT: D 760 LEU cc_start: 0.7859 (mp) cc_final: 0.7483 (mp) outliers start: 59 outliers final: 14 residues processed: 352 average time/residue: 1.3530 time to fit residues: 544.0424 Evaluate side-chains 313 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 287 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain 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 343 MET 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 71 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 249 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN B 711 GLN D 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115654 restraints weight = 23828.380| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.16 r_work: 0.3241 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22996 Z= 0.107 Angle : 0.447 7.419 31072 Z= 0.223 Chirality : 0.034 0.147 3468 Planarity : 0.003 0.044 3812 Dihedral : 12.788 179.961 3612 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.22 % Allowed : 13.76 % Favored : 84.02 % 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: 2.80 (0.16), residues: 2628 helix: 2.44 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : 0.06 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.003 0.001 HIS B 92 PHE 0.015 0.001 PHE C 341 TYR 0.011 0.001 TYR A 524 ARG 0.003 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1484) hydrogen bonds : angle 3.68334 ( 4344) metal coordination : bond 0.00270 ( 16) metal coordination : angle 0.85677 ( 12) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.53196 ( 8) covalent geometry : bond 0.00235 (22976) covalent geometry : angle 0.44717 (31052) *********************** 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 356 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 2.636 Fit side-chains REVERT: A 79 GLU cc_start: 0.7973 (tt0) cc_final: 0.6961 (mm-30) REVERT: A 170 ARG cc_start: 0.7828 (ttm170) cc_final: 0.6557 (pmt170) REVERT: A 222 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7432 (mtm-85) REVERT: A 257 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: A 361 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7736 (tttt) REVERT: A 380 MET cc_start: 0.7412 (mtm) cc_final: 0.7142 (mmp) REVERT: A 382 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7420 (mp) REVERT: A 393 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5370 (mt) REVERT: A 429 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: A 512 ARG cc_start: 0.7543 (tpt90) cc_final: 0.7191 (tpp80) REVERT: A 529 LEU cc_start: 0.8027 (tp) cc_final: 0.7740 (mt) REVERT: A 551 ASN cc_start: 0.8508 (t0) cc_final: 0.8155 (t0) REVERT: A 728 MET cc_start: 0.7184 (mmt) cc_final: 0.6754 (mmp) REVERT: A 756 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6559 (mt-10) REVERT: B 79 GLU cc_start: 0.7996 (tt0) cc_final: 0.6982 (mm-30) REVERT: B 170 ARG cc_start: 0.7836 (ttm170) cc_final: 0.6559 (pmt170) REVERT: B 222 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7435 (mtm-85) REVERT: B 257 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: B 380 MET cc_start: 0.7420 (mtm) cc_final: 0.7148 (mmp) REVERT: B 393 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5338 (mt) REVERT: B 429 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: B 512 ARG cc_start: 0.7546 (tpt90) cc_final: 0.7216 (tpp80) REVERT: B 529 LEU cc_start: 0.8015 (tp) cc_final: 0.7747 (mt) REVERT: B 551 ASN cc_start: 0.8504 (t0) cc_final: 0.8090 (t0) REVERT: B 570 GLU cc_start: 0.8580 (tp30) cc_final: 0.8283 (mm-30) REVERT: B 728 MET cc_start: 0.7220 (mmt) cc_final: 0.6791 (mmp) REVERT: B 756 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6554 (mt-10) REVERT: C 66 MET cc_start: 0.8078 (mmm) cc_final: 0.7819 (mmm) REVERT: C 79 GLU cc_start: 0.7981 (tt0) cc_final: 0.6971 (mm-30) REVERT: C 167 THR cc_start: 0.8394 (p) cc_final: 0.8178 (m) REVERT: C 170 ARG cc_start: 0.7828 (ttm170) cc_final: 0.6538 (pmt170) REVERT: C 222 ARG cc_start: 0.7966 (ptp-170) cc_final: 0.7454 (mtm-85) REVERT: C 361 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7774 (tttt) REVERT: C 380 MET cc_start: 0.7454 (mtm) cc_final: 0.7197 (mmp) REVERT: C 393 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5358 (mt) REVERT: C 429 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: C 512 ARG cc_start: 0.7560 (tpt90) cc_final: 0.7194 (tpp80) REVERT: C 529 LEU cc_start: 0.7975 (tp) cc_final: 0.7713 (mt) REVERT: C 551 ASN cc_start: 0.8504 (t0) cc_final: 0.8091 (t0) REVERT: C 728 MET cc_start: 0.7192 (mmt) cc_final: 0.6761 (mmp) REVERT: C 756 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6554 (mt-10) REVERT: D 66 MET cc_start: 0.8021 (mmm) cc_final: 0.7812 (mmm) REVERT: D 79 GLU cc_start: 0.7990 (tt0) cc_final: 0.6976 (mm-30) REVERT: D 170 ARG cc_start: 0.7834 (ttm170) cc_final: 0.6566 (pmt170) REVERT: D 222 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7439 (mtm-85) REVERT: D 361 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7745 (tttt) REVERT: D 380 MET cc_start: 0.7460 (mtm) cc_final: 0.7198 (mmp) REVERT: D 393 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5360 (mt) REVERT: D 429 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: D 512 ARG cc_start: 0.7544 (tpt90) cc_final: 0.7182 (tpp80) REVERT: D 529 LEU cc_start: 0.7952 (tp) cc_final: 0.7693 (mt) REVERT: D 551 ASN cc_start: 0.8506 (t0) cc_final: 0.8147 (t0) REVERT: D 728 MET cc_start: 0.7159 (mmt) cc_final: 0.6729 (mmp) REVERT: D 756 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6545 (mt-10) outliers start: 53 outliers final: 9 residues processed: 341 average time/residue: 1.3266 time to fit residues: 519.5982 Evaluate side-chains 301 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 429 GLU 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 429 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 515 LEU 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 429 GLU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 224 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 0.0050 chunk 242 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- 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 C 533 ASN D 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112829 restraints weight = 24229.770| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.19 r_work: 0.3197 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22996 Z= 0.161 Angle : 0.491 7.688 31072 Z= 0.246 Chirality : 0.036 0.155 3468 Planarity : 0.004 0.047 3812 Dihedral : 12.337 177.156 3612 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.85 % Allowed : 13.72 % Favored : 83.43 % 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: 2.63 (0.16), residues: 2628 helix: 2.32 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 315 HIS 0.003 0.001 HIS B 92 PHE 0.015 0.002 PHE C 341 TYR 0.018 0.001 TYR D 524 ARG 0.002 0.000 ARG D 191 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 1484) hydrogen bonds : angle 3.70996 ( 4344) metal coordination : bond 0.00378 ( 16) metal coordination : angle 0.49631 ( 12) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.52613 ( 8) covalent geometry : bond 0.00386 (22976) covalent geometry : angle 0.49115 (31052) *********************** 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 384 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7015 (pt0) cc_final: 0.6809 (mt0) REVERT: A 79 GLU cc_start: 0.8029 (tt0) cc_final: 0.7045 (mm-30) REVERT: A 81 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5852 (tm-30) REVERT: A 222 ARG cc_start: 0.8039 (ptp-170) cc_final: 0.7530 (mtm-85) REVERT: A 238 LYS cc_start: 0.7440 (ttpp) cc_final: 0.7127 (ttmm) REVERT: A 257 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: A 361 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7791 (tttt) REVERT: A 380 MET cc_start: 0.7534 (mtm) cc_final: 0.7197 (mmp) REVERT: A 393 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5355 (mt) REVERT: A 422 MET cc_start: 0.7564 (tpp) cc_final: 0.6813 (ttp) REVERT: A 512 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7416 (tpp80) REVERT: A 551 ASN cc_start: 0.8587 (t0) cc_final: 0.8298 (t0) REVERT: A 728 MET cc_start: 0.7372 (mmt) cc_final: 0.6906 (mmp) REVERT: A 756 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6773 (mt-10) REVERT: B 21 GLN cc_start: 0.7010 (pt0) cc_final: 0.6803 (mt0) REVERT: B 79 GLU cc_start: 0.8046 (tt0) cc_final: 0.7052 (mm-30) REVERT: B 222 ARG cc_start: 0.8034 (ptp-170) cc_final: 0.7524 (mtm-85) REVERT: B 238 LYS cc_start: 0.7446 (ttpp) cc_final: 0.7135 (ttmm) REVERT: B 257 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: B 380 MET cc_start: 0.7566 (mtm) cc_final: 0.7237 (mmp) REVERT: B 393 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5401 (mt) REVERT: B 422 MET cc_start: 0.7584 (tpp) cc_final: 0.6805 (ttp) REVERT: B 512 ARG cc_start: 0.7864 (tpt90) cc_final: 0.7405 (tpp80) REVERT: B 551 ASN cc_start: 0.8496 (t0) cc_final: 0.8097 (t0) REVERT: B 570 GLU cc_start: 0.8630 (tp30) cc_final: 0.8327 (mm-30) REVERT: B 728 MET cc_start: 0.7365 (mmt) cc_final: 0.6904 (mmp) REVERT: B 756 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6808 (mt-10) REVERT: C 21 GLN cc_start: 0.7006 (pt0) cc_final: 0.6793 (mt0) REVERT: C 79 GLU cc_start: 0.8042 (tt0) cc_final: 0.7067 (mm-30) REVERT: C 81 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5928 (tm-30) REVERT: C 222 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7532 (mtm-85) REVERT: C 238 LYS cc_start: 0.7447 (ttpp) cc_final: 0.7138 (ttmm) REVERT: C 361 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7804 (tttt) REVERT: C 380 MET cc_start: 0.7566 (mtm) cc_final: 0.7241 (mmp) REVERT: C 393 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5405 (mt) REVERT: C 422 MET cc_start: 0.7610 (tpp) cc_final: 0.6863 (ttp) REVERT: C 512 ARG cc_start: 0.7875 (tpt90) cc_final: 0.7409 (tpp80) REVERT: C 551 ASN cc_start: 0.8571 (t0) cc_final: 0.8276 (t0) REVERT: C 728 MET cc_start: 0.7373 (mmt) cc_final: 0.6915 (mmp) REVERT: C 756 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6805 (mt-10) REVERT: D 21 GLN cc_start: 0.7014 (pt0) cc_final: 0.6803 (mt0) REVERT: D 79 GLU cc_start: 0.8043 (tt0) cc_final: 0.7063 (mm-30) REVERT: D 81 GLU cc_start: 0.6492 (mt-10) cc_final: 0.5927 (tm-30) REVERT: D 222 ARG cc_start: 0.8042 (ptp-170) cc_final: 0.7530 (mtm-85) REVERT: D 238 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7134 (ttmm) REVERT: D 361 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7840 (tttt) REVERT: D 380 MET cc_start: 0.7570 (mtm) cc_final: 0.7241 (mmp) REVERT: D 393 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5352 (mt) REVERT: D 422 MET cc_start: 0.7608 (tpp) cc_final: 0.6831 (ttp) REVERT: D 512 ARG cc_start: 0.7865 (tpt90) cc_final: 0.7405 (tpp80) REVERT: D 551 ASN cc_start: 0.8575 (t0) cc_final: 0.8279 (t0) REVERT: D 728 MET cc_start: 0.7364 (mmt) cc_final: 0.6900 (mmp) REVERT: D 756 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6725 (mt-10) outliers start: 68 outliers final: 19 residues processed: 359 average time/residue: 1.2718 time to fit residues: 525.2250 Evaluate side-chains 323 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 257 ASP 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 717 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4214 > 50: distance: 52 - 73: 8.057 distance: 57 - 80: 10.525 distance: 62 - 89: 4.652 distance: 66 - 73: 6.512 distance: 73 - 74: 7.005 distance: 74 - 75: 11.852 distance: 74 - 77: 3.165 distance: 75 - 76: 9.782 distance: 75 - 80: 9.578 distance: 77 - 78: 9.940 distance: 77 - 79: 15.956 distance: 81 - 82: 6.227 distance: 81 - 84: 9.213 distance: 82 - 83: 16.714 distance: 82 - 89: 3.148 distance: 84 - 85: 8.178 distance: 85 - 86: 17.279 distance: 86 - 87: 33.223 distance: 87 - 88: 20.497 distance: 89 - 90: 8.400 distance: 90 - 91: 5.728 distance: 90 - 93: 12.369 distance: 91 - 92: 14.050 distance: 91 - 101: 10.175 distance: 93 - 94: 8.574 distance: 94 - 95: 5.068 distance: 94 - 96: 8.190 distance: 95 - 97: 6.388 distance: 96 - 98: 11.387 distance: 97 - 99: 8.780 distance: 98 - 99: 12.499 distance: 99 - 100: 5.782 distance: 101 - 102: 9.947 distance: 102 - 103: 27.970 distance: 102 - 105: 18.289 distance: 103 - 104: 11.005 distance: 103 - 109: 12.332 distance: 105 - 106: 21.858 distance: 106 - 107: 15.184 distance: 106 - 108: 15.071 distance: 109 - 110: 15.096 distance: 110 - 111: 3.103 distance: 111 - 112: 14.661 distance: 111 - 113: 21.148 distance: 113 - 114: 30.103 distance: 114 - 115: 50.338 distance: 114 - 117: 32.081 distance: 115 - 116: 44.507 distance: 115 - 119: 5.680 distance: 117 - 118: 14.328 distance: 119 - 120: 5.974 distance: 120 - 121: 60.421 distance: 120 - 123: 45.081 distance: 121 - 122: 8.789 distance: 121 - 130: 7.942 distance: 123 - 124: 33.084 distance: 124 - 125: 20.812 distance: 125 - 126: 19.222 distance: 126 - 127: 30.956 distance: 127 - 128: 20.793 distance: 127 - 129: 18.090 distance: 130 - 131: 7.423 distance: 130 - 136: 26.626 distance: 131 - 132: 9.845 distance: 131 - 134: 34.054 distance: 132 - 133: 28.937 distance: 132 - 137: 24.165 distance: 133 - 157: 30.908 distance: 134 - 135: 34.777 distance: 135 - 136: 5.557 distance: 137 - 138: 39.038 distance: 138 - 139: 22.126 distance: 138 - 141: 37.510 distance: 139 - 140: 12.036 distance: 139 - 148: 10.268 distance: 140 - 166: 17.689 distance: 141 - 142: 24.613 distance: 142 - 143: 22.492 distance: 143 - 144: 23.306 distance: 144 - 145: 4.873 distance: 145 - 146: 27.299 distance: 145 - 147: 41.840 distance: 148 - 149: 11.884 distance: 149 - 150: 33.441 distance: 149 - 152: 17.469 distance: 150 - 151: 19.658 distance: 150 - 157: 16.205 distance: 152 - 153: 16.016 distance: 153 - 154: 36.625 distance: 154 - 155: 29.705 distance: 154 - 156: 24.284