Starting phenix.real_space_refine on Sun Mar 17 03:38:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/03_2024/7lft_23306_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/03_2024/7lft_23306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/03_2024/7lft_23306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/03_2024/7lft_23306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/03_2024/7lft_23306_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/03_2024/7lft_23306_trim_updated.pdb" } resolution = 2.6 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 8 5.49 5 S 76 5.16 5 C 10280 2.51 5 N 2380 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D ARG 560": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "D" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {' K': 3, 'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.59, per 1000 atoms: 0.55 Number of scatterers: 15479 At special positions: 0 Unit cell: (95.372, 95.372, 119.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 76 16.00 P 8 15.00 O 2732 8.00 N 2380 7.00 C 10280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.04 Conformation dependent library (CDL) restraints added in 2.5 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 62.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.210A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 403 Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.684A pdb=" N TYR A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 removed outlier: 4.515A pdb=" N ASP A 482 " --> pdb=" O ILE A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 604 Processing helix chain 'B' and resid 163 through 188 Proline residue: B 175 - end of helix removed outlier: 5.210A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 325 Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'B' and resid 372 through 403 Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.683A pdb=" N TYR B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 removed outlier: 4.515A pdb=" N ASP B 482 " --> pdb=" O ILE B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 604 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 5.210A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.683A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 482 removed outlier: 4.516A pdb=" N ASP C 482 " --> pdb=" O ILE C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 604 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.210A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 253 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 403 Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 4.683A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 482 removed outlier: 4.515A pdb=" N ASP D 482 " --> pdb=" O ILE D 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 604 Processing sheet with id= A, first strand: chain 'A' and resid 496 through 498 Processing sheet with id= B, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.880A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 496 through 498 Processing sheet with id= D, first strand: chain 'B' and resid 564 through 567 removed outlier: 3.880A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 496 through 498 Processing sheet with id= F, first strand: chain 'C' and resid 564 through 567 removed outlier: 3.879A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 496 through 498 Processing sheet with id= H, first strand: chain 'D' and resid 564 through 567 removed outlier: 3.880A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 6.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2376 1.27 - 1.41: 3932 1.41 - 1.54: 9096 1.54 - 1.67: 280 1.67 - 1.80: 128 Bond restraints: 15812 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" O VAL D 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL A 370 " pdb=" O VAL A 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL B 370 " pdb=" O VAL B 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL C 370 " pdb=" O VAL C 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.98e+01 bond pdb=" C31 CPL D 706 " pdb=" O2 CPL D 706 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 15807 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.12: 273 105.12 - 112.38: 8331 112.38 - 119.63: 5078 119.63 - 126.88: 7474 126.88 - 134.14: 172 Bond angle restraints: 21328 Sorted by residual: angle pdb=" O3P CPL A 707 " pdb=" P CPL A 707 " pdb=" O4P CPL A 707 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL D 706 " pdb=" P CPL D 706 " pdb=" O4P CPL D 706 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL C 706 " pdb=" P CPL C 706 " pdb=" O4P CPL C 706 " ideal model delta sigma weight residual 93.29 116.17 -22.88 3.00e+00 1.11e-01 5.82e+01 angle pdb=" O3P CPL B 706 " pdb=" P CPL B 706 " pdb=" O4P CPL B 706 " ideal model delta sigma weight residual 93.29 116.12 -22.83 3.00e+00 1.11e-01 5.79e+01 angle pdb=" N VAL A 370 " pdb=" CA VAL A 370 " pdb=" C VAL A 370 " ideal model delta sigma weight residual 111.56 106.32 5.24 8.60e-01 1.35e+00 3.71e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 9396 27.56 - 55.12: 460 55.12 - 82.68: 44 82.68 - 110.24: 8 110.24 - 137.79: 8 Dihedral angle restraints: 9916 sinusoidal: 4592 harmonic: 5324 Sorted by residual: dihedral pdb=" C3 CPL B 706 " pdb=" C1 CPL B 706 " pdb=" C2 CPL B 706 " pdb=" O3P CPL B 706 " ideal model delta sinusoidal sigma weight residual 72.09 -150.12 -137.79 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3 CPL C 706 " pdb=" C1 CPL C 706 " pdb=" C2 CPL C 706 " pdb=" O3P CPL C 706 " ideal model delta sinusoidal sigma weight residual 72.09 -150.14 -137.77 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3 CPL A 707 " pdb=" C1 CPL A 707 " pdb=" C2 CPL A 707 " pdb=" O3P CPL A 707 " ideal model delta sinusoidal sigma weight residual 72.09 -150.14 -137.77 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 9913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2238 0.094 - 0.188: 93 0.188 - 0.282: 29 0.282 - 0.377: 0 0.377 - 0.471: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" C10 CLR A 702 " pdb=" C1 CLR A 702 " pdb=" C5 CLR A 702 " pdb=" C9 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C10 CLR C 701 " pdb=" C1 CLR C 701 " pdb=" C5 CLR C 701 " pdb=" C9 CLR C 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C10 CLR D 701 " pdb=" C1 CLR D 701 " pdb=" C5 CLR D 701 " pdb=" C9 CLR D 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2365 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 501 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO D 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 501 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 502 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 501 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.020 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.49: 69 2.49 - 3.16: 13283 3.16 - 3.82: 32568 3.82 - 4.48: 46112 4.48 - 5.14: 71641 Nonbonded interactions: 163673 Sorted by model distance: nonbonded pdb=" K K A 710 " pdb=" K K A 711 " model vdw 1.832 2.660 nonbonded pdb=" OG SER A 567 " pdb=" OG SER A 571 " model vdw 2.187 2.440 nonbonded pdb=" OG SER D 567 " pdb=" OG SER D 571 " model vdw 2.188 2.440 nonbonded pdb=" OG SER C 567 " pdb=" OG SER C 571 " model vdw 2.188 2.440 nonbonded pdb=" OG SER B 567 " pdb=" OG SER B 571 " model vdw 2.188 2.440 ... (remaining 163668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or resid 701 through 708)) 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: 1.350 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: 0.010 Extract box with map and model: 5.850 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.100 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.009 0.102 15812 Z= 0.588 Angle : 1.096 22.901 21328 Z= 0.478 Chirality : 0.057 0.471 2368 Planarity : 0.004 0.036 2552 Dihedral : 16.077 137.795 6500 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.25 % Allowed : 1.97 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.18), residues: 1792 helix: -0.10 (0.14), residues: 1176 sheet: -2.84 (1.00), residues: 20 loop : -1.13 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 168 HIS 0.003 0.001 HIS A 312 PHE 0.014 0.002 PHE D 298 TYR 0.022 0.002 TYR A 349 ARG 0.004 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 1.787 Fit side-chains REVERT: A 399 MET cc_start: 0.8352 (ttm) cc_final: 0.8068 (ttp) REVERT: A 403 MET cc_start: 0.8494 (mtp) cc_final: 0.8182 (mtp) REVERT: A 409 GLU cc_start: 0.7688 (tt0) cc_final: 0.7415 (tt0) REVERT: A 551 ASN cc_start: 0.6890 (m-40) cc_final: 0.6672 (m-40) REVERT: A 572 ASP cc_start: 0.6943 (t0) cc_final: 0.6734 (t0) REVERT: A 594 MET cc_start: 0.7125 (ttp) cc_final: 0.6524 (tmt) REVERT: A 597 GLU cc_start: 0.6597 (tm-30) cc_final: 0.6263 (tm-30) REVERT: B 399 MET cc_start: 0.8350 (ttm) cc_final: 0.8067 (ttp) REVERT: B 403 MET cc_start: 0.8494 (mtp) cc_final: 0.8182 (mtp) REVERT: B 409 GLU cc_start: 0.7687 (tt0) cc_final: 0.7415 (tt0) REVERT: B 551 ASN cc_start: 0.6871 (m-40) cc_final: 0.6650 (m-40) REVERT: B 572 ASP cc_start: 0.6943 (t0) cc_final: 0.6733 (t0) REVERT: B 594 MET cc_start: 0.7131 (ttp) cc_final: 0.6534 (tmt) REVERT: B 597 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6262 (tm-30) REVERT: C 399 MET cc_start: 0.8349 (ttm) cc_final: 0.8061 (ttp) REVERT: C 403 MET cc_start: 0.8509 (mtp) cc_final: 0.8203 (mtp) REVERT: C 409 GLU cc_start: 0.7688 (tt0) cc_final: 0.7415 (tt0) REVERT: C 551 ASN cc_start: 0.6855 (m-40) cc_final: 0.6642 (m-40) REVERT: C 572 ASP cc_start: 0.6926 (t0) cc_final: 0.6697 (t0) REVERT: C 594 MET cc_start: 0.7131 (ttp) cc_final: 0.6542 (tmt) REVERT: C 597 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6227 (tm-30) REVERT: D 399 MET cc_start: 0.8350 (ttm) cc_final: 0.8066 (ttp) REVERT: D 403 MET cc_start: 0.8507 (mtp) cc_final: 0.8202 (mtp) REVERT: D 409 GLU cc_start: 0.7693 (tt0) cc_final: 0.7419 (tt0) REVERT: D 551 ASN cc_start: 0.6849 (m-40) cc_final: 0.6634 (m-40) REVERT: D 572 ASP cc_start: 0.6930 (t0) cc_final: 0.6700 (t0) REVERT: D 594 MET cc_start: 0.7134 (ttp) cc_final: 0.6549 (tmt) REVERT: D 597 GLU cc_start: 0.6532 (tm-30) cc_final: 0.6230 (tm-30) outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 1.4195 time to fit residues: 359.4697 Evaluate side-chains 173 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.0040 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 470 HIS A 534 GLN A 559 ASN B 226 GLN B 470 HIS B 534 GLN B 559 ASN C 226 GLN C 470 HIS C 534 GLN C 559 ASN D 226 GLN D 470 HIS D 534 GLN D 559 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15812 Z= 0.155 Angle : 0.445 7.737 21328 Z= 0.237 Chirality : 0.038 0.136 2368 Planarity : 0.004 0.033 2552 Dihedral : 13.206 85.989 2920 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.17 % Allowed : 7.51 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.19), residues: 1792 helix: 0.98 (0.14), residues: 1200 sheet: -2.55 (0.98), residues: 20 loop : -0.75 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 168 HIS 0.003 0.001 HIS B 312 PHE 0.010 0.001 PHE A 298 TYR 0.014 0.001 TYR C 349 ARG 0.005 0.000 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 1.773 Fit side-chains REVERT: A 399 MET cc_start: 0.8186 (ttm) cc_final: 0.7943 (ttp) REVERT: A 409 GLU cc_start: 0.7590 (tt0) cc_final: 0.7304 (tt0) REVERT: A 428 LYS cc_start: 0.7860 (mmmm) cc_final: 0.7510 (mmtm) REVERT: A 490 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: A 516 MET cc_start: 0.8843 (ttt) cc_final: 0.8553 (tmm) REVERT: A 551 ASN cc_start: 0.6873 (m-40) cc_final: 0.6267 (m110) REVERT: A 572 ASP cc_start: 0.6932 (t0) cc_final: 0.6688 (t0) REVERT: A 597 GLU cc_start: 0.6574 (tm-30) cc_final: 0.6151 (tm-30) REVERT: A 600 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6685 (ptmm) REVERT: B 281 MET cc_start: 0.8573 (ttp) cc_final: 0.8367 (ttm) REVERT: B 399 MET cc_start: 0.8186 (ttm) cc_final: 0.7940 (ttp) REVERT: B 409 GLU cc_start: 0.7590 (tt0) cc_final: 0.7303 (tt0) REVERT: B 428 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7509 (mmtm) REVERT: B 490 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7021 (tp30) REVERT: B 516 MET cc_start: 0.8849 (ttt) cc_final: 0.8557 (tmm) REVERT: B 551 ASN cc_start: 0.6954 (m-40) cc_final: 0.6340 (m110) REVERT: B 572 ASP cc_start: 0.6936 (t0) cc_final: 0.6689 (t0) REVERT: B 594 MET cc_start: 0.7128 (ttp) cc_final: 0.6647 (tmt) REVERT: B 597 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6153 (tm-30) REVERT: B 600 LYS cc_start: 0.7171 (ttpt) cc_final: 0.6672 (ptmm) REVERT: C 226 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7262 (mp-120) REVERT: C 281 MET cc_start: 0.8574 (ttp) cc_final: 0.8368 (ttm) REVERT: C 399 MET cc_start: 0.8182 (ttm) cc_final: 0.7937 (ttp) REVERT: C 409 GLU cc_start: 0.7586 (tt0) cc_final: 0.7293 (tt0) REVERT: C 428 LYS cc_start: 0.7873 (mmmm) cc_final: 0.7511 (mmtm) REVERT: C 490 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: C 516 MET cc_start: 0.8848 (ttt) cc_final: 0.8562 (tmm) REVERT: C 551 ASN cc_start: 0.6939 (m-40) cc_final: 0.6396 (m110) REVERT: C 572 ASP cc_start: 0.6920 (t0) cc_final: 0.6655 (t0) REVERT: C 597 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6165 (tm-30) REVERT: C 600 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6655 (ptmm) REVERT: D 281 MET cc_start: 0.8573 (ttp) cc_final: 0.8368 (ttm) REVERT: D 399 MET cc_start: 0.8183 (ttm) cc_final: 0.7939 (ttp) REVERT: D 409 GLU cc_start: 0.7588 (tt0) cc_final: 0.7291 (tt0) REVERT: D 428 LYS cc_start: 0.7876 (mmmm) cc_final: 0.7523 (mmtm) REVERT: D 490 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: D 516 MET cc_start: 0.8844 (ttt) cc_final: 0.8562 (tmm) REVERT: D 551 ASN cc_start: 0.6937 (m-40) cc_final: 0.6392 (m110) REVERT: D 572 ASP cc_start: 0.6879 (t0) cc_final: 0.6626 (t0) REVERT: D 597 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6160 (tm-30) REVERT: D 600 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6638 (ptmm) outliers start: 19 outliers final: 0 residues processed: 222 average time/residue: 1.3903 time to fit residues: 338.2638 Evaluate side-chains 173 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15812 Z= 0.285 Angle : 0.510 5.703 21328 Z= 0.272 Chirality : 0.041 0.144 2368 Planarity : 0.004 0.032 2552 Dihedral : 12.829 86.988 2920 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.91 % Allowed : 9.42 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.19), residues: 1792 helix: 1.17 (0.15), residues: 1200 sheet: -2.72 (0.93), residues: 20 loop : -0.56 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 168 HIS 0.005 0.002 HIS C 312 PHE 0.016 0.002 PHE D 298 TYR 0.021 0.002 TYR B 349 ARG 0.004 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.744 Fit side-chains REVERT: A 226 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7211 (mp-120) REVERT: A 399 MET cc_start: 0.8336 (ttm) cc_final: 0.8092 (ttp) REVERT: A 409 GLU cc_start: 0.7668 (tt0) cc_final: 0.7401 (tt0) REVERT: A 516 MET cc_start: 0.8926 (ttt) cc_final: 0.8626 (tmm) REVERT: A 572 ASP cc_start: 0.7004 (t0) cc_final: 0.6770 (t0) REVERT: A 597 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6180 (tm-30) REVERT: A 600 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6633 (ptmm) REVERT: B 226 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7218 (mp-120) REVERT: B 399 MET cc_start: 0.8333 (ttm) cc_final: 0.8089 (ttp) REVERT: B 409 GLU cc_start: 0.7660 (tt0) cc_final: 0.7394 (tt0) REVERT: B 516 MET cc_start: 0.8928 (ttt) cc_final: 0.8621 (tmm) REVERT: B 597 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6182 (tm-30) REVERT: B 600 LYS cc_start: 0.7100 (ttpt) cc_final: 0.6635 (ptmm) REVERT: C 399 MET cc_start: 0.8334 (ttm) cc_final: 0.8092 (ttp) REVERT: C 409 GLU cc_start: 0.7666 (tt0) cc_final: 0.7398 (tt0) REVERT: C 516 MET cc_start: 0.8927 (ttt) cc_final: 0.8625 (tmm) REVERT: C 551 ASN cc_start: 0.6982 (m-40) cc_final: 0.6355 (m110) REVERT: C 572 ASP cc_start: 0.6992 (t0) cc_final: 0.6761 (t0) REVERT: C 594 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6623 (tmt) REVERT: C 597 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6241 (tm-30) REVERT: C 600 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6670 (ptmm) REVERT: D 226 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7217 (mp-120) REVERT: D 399 MET cc_start: 0.8334 (ttm) cc_final: 0.8092 (ttp) REVERT: D 409 GLU cc_start: 0.7666 (tt0) cc_final: 0.7398 (tt0) REVERT: D 516 MET cc_start: 0.8928 (ttt) cc_final: 0.8624 (tmm) REVERT: D 551 ASN cc_start: 0.6980 (m-40) cc_final: 0.6353 (m110) REVERT: D 572 ASP cc_start: 0.6953 (t0) cc_final: 0.6730 (t0) REVERT: D 594 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6627 (tmt) REVERT: D 597 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6239 (tm-30) REVERT: D 600 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6672 (ptmm) outliers start: 31 outliers final: 5 residues processed: 197 average time/residue: 1.4443 time to fit residues: 310.6569 Evaluate side-chains 175 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 329 ASN A 551 ASN B 226 GLN B 329 ASN B 551 ASN C 329 ASN D 226 GLN D 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15812 Z= 0.259 Angle : 0.491 5.400 21328 Z= 0.264 Chirality : 0.040 0.147 2368 Planarity : 0.004 0.033 2552 Dihedral : 12.545 85.100 2920 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.77 % Allowed : 10.04 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.19), residues: 1792 helix: 1.35 (0.15), residues: 1200 sheet: -2.67 (0.92), residues: 20 loop : -0.43 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 168 HIS 0.005 0.002 HIS A 312 PHE 0.016 0.002 PHE C 298 TYR 0.020 0.002 TYR C 349 ARG 0.003 0.000 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 1.807 Fit side-chains REVERT: A 399 MET cc_start: 0.8288 (ttm) cc_final: 0.8049 (ttp) REVERT: A 409 GLU cc_start: 0.7670 (tt0) cc_final: 0.7409 (tt0) REVERT: A 431 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: A 490 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: A 516 MET cc_start: 0.8915 (ttt) cc_final: 0.8625 (tmm) REVERT: A 597 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6211 (tm-30) REVERT: A 600 LYS cc_start: 0.7060 (ttpt) cc_final: 0.6585 (ptmm) REVERT: B 226 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7200 (mp-120) REVERT: B 399 MET cc_start: 0.8286 (ttm) cc_final: 0.8029 (ttp) REVERT: B 409 GLU cc_start: 0.7670 (tt0) cc_final: 0.7410 (tt0) REVERT: B 431 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: B 490 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6909 (tp30) REVERT: B 516 MET cc_start: 0.8917 (ttt) cc_final: 0.8625 (tmm) REVERT: B 597 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6209 (tm-30) REVERT: B 600 LYS cc_start: 0.7070 (ttpt) cc_final: 0.6596 (ptmm) REVERT: C 399 MET cc_start: 0.8287 (ttm) cc_final: 0.8029 (ttp) REVERT: C 409 GLU cc_start: 0.7661 (tt0) cc_final: 0.7397 (tt0) REVERT: C 431 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: C 490 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: C 516 MET cc_start: 0.8918 (ttt) cc_final: 0.8626 (tmm) REVERT: C 551 ASN cc_start: 0.7008 (m-40) cc_final: 0.6309 (m110) REVERT: C 594 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6673 (tmt) REVERT: C 597 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6249 (tm-30) REVERT: C 600 LYS cc_start: 0.7105 (ttpt) cc_final: 0.6652 (ptmm) REVERT: D 226 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7202 (mp-120) REVERT: D 399 MET cc_start: 0.8288 (ttm) cc_final: 0.8029 (ttp) REVERT: D 409 GLU cc_start: 0.7662 (tt0) cc_final: 0.7398 (tt0) REVERT: D 431 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: D 490 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: D 516 MET cc_start: 0.8919 (ttt) cc_final: 0.8624 (tmm) REVERT: D 551 ASN cc_start: 0.7006 (m-40) cc_final: 0.6307 (m110) REVERT: D 594 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6677 (tmt) REVERT: D 597 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6245 (tm-30) REVERT: D 600 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6653 (ptmm) outliers start: 45 outliers final: 20 residues processed: 196 average time/residue: 1.4396 time to fit residues: 308.7171 Evaluate side-chains 191 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15812 Z= 0.149 Angle : 0.427 5.248 21328 Z= 0.229 Chirality : 0.038 0.145 2368 Planarity : 0.003 0.033 2552 Dihedral : 11.158 72.395 2920 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.22 % Allowed : 10.78 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.20), residues: 1792 helix: 1.63 (0.15), residues: 1204 sheet: -2.32 (0.95), residues: 20 loop : -0.34 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.002 0.001 HIS C 312 PHE 0.012 0.001 PHE A 298 TYR 0.014 0.001 TYR C 349 ARG 0.003 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.896 Fit side-chains REVERT: A 174 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 399 MET cc_start: 0.8170 (ttm) cc_final: 0.7864 (ttp) REVERT: A 409 GLU cc_start: 0.7599 (tt0) cc_final: 0.7327 (tt0) REVERT: A 428 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7405 (mptp) REVERT: A 431 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 516 MET cc_start: 0.8812 (ttt) cc_final: 0.8556 (tmm) REVERT: A 597 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6405 (tp30) REVERT: A 600 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6695 (mtmt) REVERT: B 174 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 399 MET cc_start: 0.8169 (ttm) cc_final: 0.7859 (ttp) REVERT: B 409 GLU cc_start: 0.7598 (tt0) cc_final: 0.7327 (tt0) REVERT: B 428 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7404 (mptp) REVERT: B 431 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: B 516 MET cc_start: 0.8817 (ttt) cc_final: 0.8558 (tmm) REVERT: B 597 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6402 (tp30) REVERT: B 600 LYS cc_start: 0.7097 (ttpt) cc_final: 0.6699 (mtmt) REVERT: C 174 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8341 (mp) REVERT: C 399 MET cc_start: 0.8172 (ttm) cc_final: 0.7865 (ttp) REVERT: C 409 GLU cc_start: 0.7596 (tt0) cc_final: 0.7323 (tt0) REVERT: C 428 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7400 (mptp) REVERT: C 431 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: C 516 MET cc_start: 0.8813 (ttt) cc_final: 0.8559 (tmm) REVERT: C 551 ASN cc_start: 0.6999 (m-40) cc_final: 0.6324 (m110) REVERT: C 594 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6664 (tmt) REVERT: C 600 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6797 (mtmt) REVERT: D 174 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8340 (mp) REVERT: D 399 MET cc_start: 0.8171 (ttm) cc_final: 0.7863 (ttp) REVERT: D 409 GLU cc_start: 0.7594 (tt0) cc_final: 0.7320 (tt0) REVERT: D 428 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7394 (mptp) REVERT: D 431 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: D 551 ASN cc_start: 0.6997 (m-40) cc_final: 0.6322 (m110) REVERT: D 594 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6659 (tmt) REVERT: D 600 LYS cc_start: 0.7157 (ttpt) cc_final: 0.6783 (mtmt) outliers start: 36 outliers final: 8 residues processed: 195 average time/residue: 1.4011 time to fit residues: 299.1777 Evaluate side-chains 179 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 534 GLN B 226 GLN B 329 ASN C 329 ASN D 226 GLN D 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15812 Z= 0.142 Angle : 0.421 5.284 21328 Z= 0.226 Chirality : 0.038 0.146 2368 Planarity : 0.003 0.034 2552 Dihedral : 10.407 71.847 2920 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.16 % Allowed : 11.45 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.20), residues: 1792 helix: 1.79 (0.15), residues: 1204 sheet: -2.22 (0.94), residues: 20 loop : -0.21 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.003 0.001 HIS B 312 PHE 0.012 0.001 PHE A 298 TYR 0.013 0.001 TYR D 349 ARG 0.003 0.000 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.841 Fit side-chains REVERT: A 174 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 399 MET cc_start: 0.8149 (ttm) cc_final: 0.7844 (ttp) REVERT: A 409 GLU cc_start: 0.7595 (tt0) cc_final: 0.7335 (tt0) REVERT: A 428 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7421 (mptp) REVERT: A 431 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: A 597 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6397 (tp30) REVERT: A 600 LYS cc_start: 0.7114 (ttpt) cc_final: 0.6708 (mtmt) REVERT: B 174 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8332 (mp) REVERT: B 226 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7195 (mp-120) REVERT: B 399 MET cc_start: 0.8150 (ttm) cc_final: 0.7846 (ttp) REVERT: B 409 GLU cc_start: 0.7597 (tt0) cc_final: 0.7336 (tt0) REVERT: B 428 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7422 (mptp) REVERT: B 431 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: B 516 MET cc_start: 0.8804 (ttt) cc_final: 0.8541 (tmm) REVERT: B 597 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6396 (tp30) REVERT: B 600 LYS cc_start: 0.7114 (ttpt) cc_final: 0.6708 (mtmt) REVERT: C 174 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 399 MET cc_start: 0.8136 (ttm) cc_final: 0.7838 (ttp) REVERT: C 409 GLU cc_start: 0.7596 (tt0) cc_final: 0.7333 (tt0) REVERT: C 428 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7419 (mptp) REVERT: C 431 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: C 551 ASN cc_start: 0.6993 (m-40) cc_final: 0.6344 (m110) REVERT: C 594 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6634 (tmt) REVERT: C 597 GLU cc_start: 0.6699 (tp30) cc_final: 0.6447 (tp30) REVERT: C 600 LYS cc_start: 0.7161 (ttpt) cc_final: 0.6705 (ptmm) REVERT: D 174 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8331 (mp) REVERT: D 226 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7198 (mp-120) REVERT: D 399 MET cc_start: 0.8147 (ttm) cc_final: 0.7846 (ttp) REVERT: D 409 GLU cc_start: 0.7593 (tt0) cc_final: 0.7329 (tt0) REVERT: D 428 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7428 (mptp) REVERT: D 431 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 516 MET cc_start: 0.8845 (ttt) cc_final: 0.8474 (tmm) REVERT: D 551 ASN cc_start: 0.6994 (m-40) cc_final: 0.6348 (m110) REVERT: D 594 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6643 (tmt) REVERT: D 597 GLU cc_start: 0.6699 (tp30) cc_final: 0.6445 (tp30) REVERT: D 600 LYS cc_start: 0.7162 (ttpt) cc_final: 0.6703 (ptmm) outliers start: 35 outliers final: 15 residues processed: 212 average time/residue: 1.3903 time to fit residues: 322.6180 Evaluate side-chains 181 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 329 ASN A 534 GLN A 551 ASN B 226 GLN B 329 ASN B 534 GLN B 551 ASN C 329 ASN C 534 GLN D 226 GLN D 329 ASN D 534 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15812 Z= 0.277 Angle : 0.514 5.469 21328 Z= 0.275 Chirality : 0.041 0.146 2368 Planarity : 0.004 0.033 2552 Dihedral : 11.799 77.308 2920 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.14 % Allowed : 11.21 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.20), residues: 1792 helix: 1.63 (0.15), residues: 1200 sheet: -2.70 (0.88), residues: 20 loop : -0.31 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 168 HIS 0.005 0.002 HIS C 312 PHE 0.017 0.002 PHE A 298 TYR 0.022 0.002 TYR B 349 ARG 0.002 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 157 time to evaluate : 1.898 Fit side-chains REVERT: A 399 MET cc_start: 0.8285 (ttm) cc_final: 0.8020 (ttp) REVERT: A 409 GLU cc_start: 0.7684 (tt0) cc_final: 0.7417 (tt0) REVERT: A 428 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7388 (mptp) REVERT: A 431 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: A 597 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6520 (tp30) REVERT: A 600 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6682 (mtmt) REVERT: B 174 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 226 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7241 (mp-120) REVERT: B 399 MET cc_start: 0.8284 (ttm) cc_final: 0.8019 (ttp) REVERT: B 409 GLU cc_start: 0.7686 (tt0) cc_final: 0.7419 (tt0) REVERT: B 428 LYS cc_start: 0.7921 (mmmm) cc_final: 0.7391 (mptp) REVERT: B 431 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: B 597 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6522 (tp30) REVERT: B 600 LYS cc_start: 0.7088 (ttpt) cc_final: 0.6682 (mtmt) REVERT: C 174 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8229 (mp) REVERT: C 226 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7179 (mp-120) REVERT: C 399 MET cc_start: 0.8286 (ttm) cc_final: 0.8020 (ttp) REVERT: C 409 GLU cc_start: 0.7676 (tt0) cc_final: 0.7408 (tt0) REVERT: C 428 LYS cc_start: 0.7921 (mmmm) cc_final: 0.7386 (mptp) REVERT: C 431 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: C 516 MET cc_start: 0.8902 (ttt) cc_final: 0.8545 (tmm) REVERT: C 551 ASN cc_start: 0.7019 (m-40) cc_final: 0.6283 (m110) REVERT: C 594 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6610 (tmt) REVERT: C 597 GLU cc_start: 0.6655 (tp30) cc_final: 0.6342 (tp30) REVERT: C 600 LYS cc_start: 0.7145 (ttpt) cc_final: 0.6651 (ptmm) REVERT: D 174 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8267 (mp) REVERT: D 226 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7244 (mp-120) REVERT: D 399 MET cc_start: 0.8279 (ttm) cc_final: 0.8014 (ttp) REVERT: D 409 GLU cc_start: 0.7675 (tt0) cc_final: 0.7406 (tt0) REVERT: D 428 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7389 (mptp) REVERT: D 431 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: D 551 ASN cc_start: 0.7020 (m-40) cc_final: 0.6281 (m110) REVERT: D 594 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6603 (tmt) REVERT: D 600 LYS cc_start: 0.7145 (ttpt) cc_final: 0.6653 (ptmm) outliers start: 51 outliers final: 20 residues processed: 198 average time/residue: 1.3448 time to fit residues: 292.4024 Evaluate side-chains 185 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 226 GLN B 551 ASN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15812 Z= 0.244 Angle : 0.501 8.112 21328 Z= 0.266 Chirality : 0.040 0.147 2368 Planarity : 0.004 0.034 2552 Dihedral : 11.624 76.462 2920 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.65 % Allowed : 11.64 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.20), residues: 1792 helix: 1.61 (0.15), residues: 1200 sheet: -2.80 (0.85), residues: 20 loop : -0.33 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 168 HIS 0.005 0.002 HIS A 312 PHE 0.016 0.002 PHE B 298 TYR 0.019 0.002 TYR C 349 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 1.879 Fit side-chains REVERT: A 174 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 399 MET cc_start: 0.8263 (ttm) cc_final: 0.8008 (ttp) REVERT: A 409 GLU cc_start: 0.7686 (tt0) cc_final: 0.7414 (tt0) REVERT: A 428 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7398 (mptp) REVERT: A 431 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: A 597 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6519 (tp30) REVERT: A 600 LYS cc_start: 0.7079 (ttpt) cc_final: 0.6678 (mtmt) REVERT: B 174 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 226 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7293 (mp-120) REVERT: B 399 MET cc_start: 0.8261 (ttm) cc_final: 0.8006 (ttp) REVERT: B 409 GLU cc_start: 0.7687 (tt0) cc_final: 0.7415 (tt0) REVERT: B 428 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7395 (mptp) REVERT: B 431 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 597 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6523 (tp30) REVERT: B 600 LYS cc_start: 0.7079 (ttpt) cc_final: 0.6681 (mtmt) REVERT: C 174 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 399 MET cc_start: 0.8260 (ttm) cc_final: 0.8007 (ttp) REVERT: C 409 GLU cc_start: 0.7673 (tt0) cc_final: 0.7409 (tt0) REVERT: C 428 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7398 (mptp) REVERT: C 431 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: C 516 MET cc_start: 0.8896 (ttt) cc_final: 0.8536 (tmm) REVERT: C 551 ASN cc_start: 0.7016 (m-40) cc_final: 0.6290 (m110) REVERT: C 594 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6656 (tmt) REVERT: C 600 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6661 (ptmm) REVERT: D 174 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8321 (mp) REVERT: D 226 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7292 (mp-120) REVERT: D 399 MET cc_start: 0.8262 (ttm) cc_final: 0.8007 (ttp) REVERT: D 409 GLU cc_start: 0.7672 (tt0) cc_final: 0.7407 (tt0) REVERT: D 428 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7397 (mptp) REVERT: D 431 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: D 516 MET cc_start: 0.8910 (ttt) cc_final: 0.8545 (tmm) REVERT: D 551 ASN cc_start: 0.7018 (m-40) cc_final: 0.6294 (m110) REVERT: D 594 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6657 (tmt) REVERT: D 597 GLU cc_start: 0.6675 (tp30) cc_final: 0.6347 (tp30) REVERT: D 600 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6658 (ptmm) outliers start: 43 outliers final: 20 residues processed: 188 average time/residue: 1.3771 time to fit residues: 283.5364 Evaluate side-chains 180 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.0980 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 226 GLN B 329 ASN C 329 ASN D 226 GLN D 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15812 Z= 0.162 Angle : 0.450 7.848 21328 Z= 0.239 Chirality : 0.038 0.144 2368 Planarity : 0.003 0.035 2552 Dihedral : 10.694 72.376 2920 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.59 % Allowed : 11.76 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.20), residues: 1792 helix: 1.72 (0.15), residues: 1204 sheet: -2.64 (0.85), residues: 20 loop : -0.26 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 168 HIS 0.003 0.001 HIS B 312 PHE 0.012 0.001 PHE A 298 TYR 0.015 0.001 TYR C 349 ARG 0.002 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 152 time to evaluate : 1.935 Fit side-chains REVERT: A 174 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 399 MET cc_start: 0.8175 (ttm) cc_final: 0.7883 (ttp) REVERT: A 409 GLU cc_start: 0.7615 (tt0) cc_final: 0.7337 (tt0) REVERT: A 428 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7395 (mptp) REVERT: A 431 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: A 490 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: A 597 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6485 (tp30) REVERT: A 600 LYS cc_start: 0.7094 (ttpt) cc_final: 0.6712 (mtmt) REVERT: B 174 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8333 (mp) REVERT: B 226 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7213 (mp-120) REVERT: B 399 MET cc_start: 0.8183 (ttm) cc_final: 0.7891 (ttp) REVERT: B 409 GLU cc_start: 0.7620 (tt0) cc_final: 0.7341 (tt0) REVERT: B 428 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7393 (mptp) REVERT: B 431 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: B 490 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: B 597 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6478 (tp30) REVERT: B 600 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6717 (mtmt) REVERT: C 174 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 399 MET cc_start: 0.8176 (ttm) cc_final: 0.7884 (ttp) REVERT: C 409 GLU cc_start: 0.7619 (tt0) cc_final: 0.7337 (tt0) REVERT: C 428 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7394 (mptp) REVERT: C 431 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: C 490 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6932 (tp30) REVERT: C 516 MET cc_start: 0.8848 (ttt) cc_final: 0.8489 (tmm) REVERT: C 551 ASN cc_start: 0.7034 (m-40) cc_final: 0.6329 (m110) REVERT: C 594 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6640 (tmt) REVERT: C 597 GLU cc_start: 0.6697 (tp30) cc_final: 0.6423 (tp30) REVERT: C 600 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6675 (ptmm) REVERT: D 174 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8334 (mp) REVERT: D 226 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7216 (mp-120) REVERT: D 399 MET cc_start: 0.8186 (ttm) cc_final: 0.7892 (ttp) REVERT: D 409 GLU cc_start: 0.7616 (tt0) cc_final: 0.7338 (tt0) REVERT: D 428 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7384 (mptp) REVERT: D 431 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: D 490 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: D 516 MET cc_start: 0.8854 (ttt) cc_final: 0.8497 (tmm) REVERT: D 551 ASN cc_start: 0.7021 (m-40) cc_final: 0.6316 (m110) REVERT: D 594 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6640 (tmt) REVERT: D 597 GLU cc_start: 0.6696 (tp30) cc_final: 0.6421 (tp30) REVERT: D 600 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6675 (ptmm) outliers start: 42 outliers final: 16 residues processed: 186 average time/residue: 1.4110 time to fit residues: 287.9689 Evaluate side-chains 178 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 329 ASN B 226 GLN B 329 ASN C 329 ASN D 226 GLN D 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15812 Z= 0.161 Angle : 0.451 7.799 21328 Z= 0.240 Chirality : 0.038 0.144 2368 Planarity : 0.003 0.035 2552 Dihedral : 10.524 72.796 2920 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.83 % Allowed : 12.07 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.20), residues: 1792 helix: 1.71 (0.15), residues: 1204 sheet: -2.58 (0.84), residues: 20 loop : -0.22 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 168 HIS 0.003 0.001 HIS A 312 PHE 0.012 0.001 PHE B 298 TYR 0.015 0.001 TYR B 349 ARG 0.002 0.000 ARG C 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 1.553 Fit side-chains REVERT: A 174 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 399 MET cc_start: 0.8166 (ttm) cc_final: 0.7885 (ttp) REVERT: A 409 GLU cc_start: 0.7606 (tt0) cc_final: 0.7335 (tt0) REVERT: A 428 LYS cc_start: 0.7954 (mmmm) cc_final: 0.7448 (mptp) REVERT: A 431 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: A 490 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: A 597 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6456 (tp30) REVERT: A 600 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6713 (mtmt) REVERT: B 174 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 226 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7162 (mp-120) REVERT: B 399 MET cc_start: 0.8166 (ttm) cc_final: 0.7884 (ttp) REVERT: B 409 GLU cc_start: 0.7608 (tt0) cc_final: 0.7337 (tt0) REVERT: B 428 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7403 (mptp) REVERT: B 431 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: B 490 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: B 600 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6716 (mtmt) REVERT: C 174 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8319 (mp) REVERT: C 399 MET cc_start: 0.8164 (ttm) cc_final: 0.7884 (ttp) REVERT: C 409 GLU cc_start: 0.7605 (tt0) cc_final: 0.7333 (tt0) REVERT: C 428 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7447 (mptp) REVERT: C 431 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: C 490 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: C 516 MET cc_start: 0.8833 (ttt) cc_final: 0.8481 (tmm) REVERT: C 551 ASN cc_start: 0.7010 (m-40) cc_final: 0.6344 (m110) REVERT: C 594 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6636 (tmt) REVERT: C 597 GLU cc_start: 0.6700 (tp30) cc_final: 0.6435 (tp30) REVERT: C 600 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6688 (ptmm) REVERT: D 174 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8321 (mp) REVERT: D 226 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7166 (mp-120) REVERT: D 399 MET cc_start: 0.8165 (ttm) cc_final: 0.7883 (ttp) REVERT: D 409 GLU cc_start: 0.7604 (tt0) cc_final: 0.7333 (tt0) REVERT: D 428 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7446 (mptp) REVERT: D 431 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: D 490 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6943 (tp30) REVERT: D 551 ASN cc_start: 0.7010 (m-40) cc_final: 0.6343 (m110) REVERT: D 594 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6631 (tmt) REVERT: D 597 GLU cc_start: 0.6700 (tp30) cc_final: 0.6439 (tp30) REVERT: D 600 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6686 (ptmm) outliers start: 46 outliers final: 23 residues processed: 188 average time/residue: 1.4040 time to fit residues: 289.8646 Evaluate side-chains 188 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106298 restraints weight = 17846.374| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.14 r_work: 0.3109 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15812 Z= 0.136 Angle : 0.435 7.670 21328 Z= 0.231 Chirality : 0.038 0.143 2368 Planarity : 0.003 0.035 2552 Dihedral : 9.950 70.485 2920 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.52 % Allowed : 12.44 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.20), residues: 1792 helix: 1.80 (0.15), residues: 1204 sheet: -2.35 (0.86), residues: 20 loop : -0.15 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 168 HIS 0.002 0.001 HIS C 312 PHE 0.011 0.001 PHE D 298 TYR 0.012 0.001 TYR C 349 ARG 0.003 0.000 ARG D 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.96 seconds wall clock time: 98 minutes 12.58 seconds (5892.58 seconds total)