Starting phenix.real_space_refine on Sat Feb 17 02:41:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/02_2024/6bo5_7119.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/02_2024/6bo5_7119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/02_2024/6bo5_7119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/02_2024/6bo5_7119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/02_2024/6bo5_7119.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/02_2024/6bo5_7119.pdb" } resolution = 3.6 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= 0.004 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 11280 2.51 5 N 2900 2.21 5 O 2960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17236 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Time building chain proxies: 9.24, per 1000 atoms: 0.54 Number of scatterers: 17236 At special positions: 0 Unit cell: (136.53, 136.53, 110.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2960 8.00 N 2900 7.00 C 11280 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: 6.69 Conformation dependent library (CDL) restraints added in 3.1 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 59.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.895A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.994A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 212 through 220 removed outlier: 4.294A pdb=" N THR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 393 through 413 Processing helix chain 'A' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 536 through 557 removed outlier: 3.547A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 623 through 649 Processing helix chain 'A' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS A 661 " --> pdb=" O TRP A 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.895A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.993A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 212 through 220 removed outlier: 4.295A pdb=" N THR B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 279 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL B 373 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 389 through 392 Processing helix chain 'B' and resid 393 through 413 Processing helix chain 'B' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 536 through 557 removed outlier: 3.548A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 623 through 649 Processing helix chain 'B' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN B 655 " --> pdb=" O HIS B 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 675 " --> pdb=" O MET B 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 143 removed outlier: 3.894A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.994A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 212 through 220 removed outlier: 4.295A pdb=" N THR D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 279 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL D 373 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 393 through 413 Processing helix chain 'D' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER D 432 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 536 Processing helix chain 'D' and resid 536 through 557 removed outlier: 3.548A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 556 " --> pdb=" O ALA D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 602 Processing helix chain 'D' and resid 623 through 649 Processing helix chain 'D' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS D 661 " --> pdb=" O TRP D 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 675 " --> pdb=" O MET D 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.896A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.994A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 212 through 220 removed outlier: 4.294A pdb=" N THR C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 279 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 387 Processing helix chain 'C' and resid 389 through 392 Processing helix chain 'C' and resid 393 through 413 Processing helix chain 'C' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER C 432 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 536 Processing helix chain 'C' and resid 536 through 557 removed outlier: 3.547A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 602 Processing helix chain 'C' and resid 623 through 649 Processing helix chain 'C' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN C 655 " --> pdb=" O HIS C 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 661 " --> pdb=" O TRP C 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 675 " --> pdb=" O MET C 671 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.538A pdb=" N LEU A 689 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.537A pdb=" N LEU B 689 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.537A pdb=" N LEU D 689 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.537A pdb=" N LEU C 689 " --> pdb=" O SER C 341 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2655 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: 4.94 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5355 1.34 - 1.46: 3620 1.46 - 1.58: 8533 1.58 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 17656 Sorted by residual: bond pdb=" C GLN B 324 " pdb=" N PRO B 325 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.16e+01 bond pdb=" C GLN D 324 " pdb=" N PRO D 325 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.16e+01 bond pdb=" C GLN A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.334 1.413 -0.079 2.34e-02 1.83e+03 1.15e+01 bond pdb=" C GLN C 324 " pdb=" N PRO C 325 " ideal model delta sigma weight residual 1.334 1.413 -0.079 2.34e-02 1.83e+03 1.15e+01 bond pdb=" CA PHE A 519 " pdb=" CB PHE A 519 " ideal model delta sigma weight residual 1.521 1.564 -0.043 1.48e-02 4.57e+03 8.42e+00 ... (remaining 17651 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 328 105.96 - 112.98: 9190 112.98 - 119.99: 6486 119.99 - 127.01: 7776 127.01 - 134.03: 232 Bond angle restraints: 24012 Sorted by residual: angle pdb=" N VAL B 621 " pdb=" CA VAL B 621 " pdb=" C VAL B 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL C 621 " pdb=" CA VAL C 621 " pdb=" C VAL C 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL A 621 " pdb=" CA VAL A 621 " pdb=" C VAL A 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL D 621 " pdb=" CA VAL D 621 " pdb=" C VAL D 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL B 390 " pdb=" CA VAL B 390 " pdb=" C VAL B 390 " ideal model delta sigma weight residual 112.35 102.48 9.87 1.41e+00 5.03e-01 4.90e+01 ... (remaining 24007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.26: 9644 19.26 - 38.53: 524 38.53 - 57.79: 92 57.79 - 77.06: 16 77.06 - 96.32: 4 Dihedral angle restraints: 10280 sinusoidal: 3792 harmonic: 6488 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N CYS B 364 " pdb=" CA CYS B 364 " ideal model delta harmonic sigma weight residual -180.00 -83.68 -96.32 0 5.00e+00 4.00e-02 3.71e+02 dihedral pdb=" CA HIS A 363 " pdb=" C HIS A 363 " pdb=" N CYS A 364 " pdb=" CA CYS A 364 " ideal model delta harmonic sigma weight residual -180.00 -83.70 -96.30 0 5.00e+00 4.00e-02 3.71e+02 dihedral pdb=" CA HIS C 363 " pdb=" C HIS C 363 " pdb=" N CYS C 364 " pdb=" CA CYS C 364 " ideal model delta harmonic sigma weight residual -180.00 -83.73 -96.27 0 5.00e+00 4.00e-02 3.71e+02 ... (remaining 10277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2504 0.092 - 0.184: 244 0.184 - 0.276: 9 0.276 - 0.368: 3 0.368 - 0.461: 4 Chirality restraints: 2764 Sorted by residual: chirality pdb=" CA VAL D 621 " pdb=" N VAL D 621 " pdb=" C VAL D 621 " pdb=" CB VAL D 621 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA VAL A 621 " pdb=" N VAL A 621 " pdb=" C VAL A 621 " pdb=" CB VAL A 621 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA VAL C 621 " pdb=" N VAL C 621 " pdb=" C VAL C 621 " pdb=" CB VAL C 621 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 2761 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 519 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE D 519 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE D 519 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN D 520 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 519 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE C 519 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE C 519 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN C 520 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 519 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C PHE A 519 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE A 519 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 520 " 0.015 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4674 2.80 - 3.33: 16020 3.33 - 3.85: 27979 3.85 - 4.38: 31364 4.38 - 4.90: 51483 Nonbonded interactions: 131520 Sorted by model distance: nonbonded pdb=" O MET C 404 " pdb=" OG1 THR C 408 " model vdw 2.277 2.440 nonbonded pdb=" O MET D 404 " pdb=" OG1 THR D 408 " model vdw 2.277 2.440 nonbonded pdb=" O MET B 404 " pdb=" OG1 THR B 408 " model vdw 2.277 2.440 nonbonded pdb=" O MET A 404 " pdb=" OG1 THR A 408 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLN C 479 " pdb=" ND2 ASN C 511 " model vdw 2.295 2.520 ... (remaining 131515 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' 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 group one per residue 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.410 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 45.420 Find NCS groups from input model: 1.090 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.005 0.080 17656 Z= 0.301 Angle : 1.082 16.507 24012 Z= 0.587 Chirality : 0.055 0.461 2764 Planarity : 0.007 0.064 2984 Dihedral : 12.892 96.321 6088 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.11 % Favored : 90.53 % Rotamer: Outliers : 1.84 % Allowed : 6.67 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 2.24 % 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: -5.44 (0.12), residues: 2196 helix: -3.76 (0.08), residues: 1188 sheet: -2.75 (0.58), residues: 40 loop : -3.32 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 496 HIS 0.007 0.002 HIS D 165 PHE 0.026 0.003 PHE B 209 TYR 0.032 0.003 TYR A 323 ARG 0.005 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 348 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.6313 (ttp) cc_final: 0.6038 (mtp) REVERT: A 634 TYR cc_start: 0.7375 (t80) cc_final: 0.6973 (t80) REVERT: B 433 MET cc_start: 0.6309 (ttp) cc_final: 0.6022 (mtp) REVERT: D 433 MET cc_start: 0.6313 (ttp) cc_final: 0.6024 (mtp) REVERT: D 529 ILE cc_start: 0.8368 (pp) cc_final: 0.8154 (pt) REVERT: C 433 MET cc_start: 0.6311 (ttp) cc_final: 0.6023 (mtp) REVERT: C 529 ILE cc_start: 0.8365 (pp) cc_final: 0.8152 (pt) outliers start: 32 outliers final: 0 residues processed: 376 average time/residue: 0.3596 time to fit residues: 188.2610 Evaluate side-chains 169 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 5.9990 chunk 166 optimal weight: 0.0470 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 259 ASN A 286 GLN A 368 ASN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS B 259 ASN B 286 GLN B 368 ASN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS D 259 ASN D 286 GLN D 368 ASN D 452 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 ASN C 251 HIS C 259 ASN C 286 GLN C 368 ASN ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17656 Z= 0.167 Angle : 0.741 10.036 24012 Z= 0.369 Chirality : 0.040 0.142 2764 Planarity : 0.005 0.049 2984 Dihedral : 7.336 41.625 2392 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.74 % Allowed : 9.08 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 1.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.16), residues: 2196 helix: -1.62 (0.13), residues: 1256 sheet: -2.65 (0.59), residues: 56 loop : -2.91 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 454 HIS 0.002 0.001 HIS D 165 PHE 0.020 0.002 PHE B 519 TYR 0.027 0.002 TYR A 323 ARG 0.005 0.001 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 210 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 16 residues processed: 263 average time/residue: 0.3113 time to fit residues: 120.5634 Evaluate side-chains 162 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 166 optimal weight: 0.0070 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 200 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 160 optimal weight: 20.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 452 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17656 Z= 0.152 Angle : 0.692 10.421 24012 Z= 0.341 Chirality : 0.039 0.156 2764 Planarity : 0.004 0.044 2984 Dihedral : 6.491 37.097 2392 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.53 % Allowed : 12.01 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2196 helix: -0.51 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -2.58 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 496 HIS 0.002 0.000 HIS B 165 PHE 0.014 0.001 PHE B 519 TYR 0.027 0.002 TYR C 525 ARG 0.006 0.000 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 ILE cc_start: 0.8083 (pt) cc_final: 0.7473 (pt) REVERT: B 529 ILE cc_start: 0.8128 (pt) cc_final: 0.7532 (pt) outliers start: 44 outliers final: 20 residues processed: 215 average time/residue: 0.2623 time to fit residues: 87.6492 Evaluate side-chains 149 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 498 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17656 Z= 0.181 Angle : 0.698 11.405 24012 Z= 0.344 Chirality : 0.039 0.130 2764 Planarity : 0.004 0.040 2984 Dihedral : 6.253 34.457 2392 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.13 % Allowed : 14.54 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -1.46 (0.17), residues: 2196 helix: 0.05 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -2.49 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 496 HIS 0.004 0.001 HIS C 165 PHE 0.013 0.001 PHE D 519 TYR 0.027 0.002 TYR D 525 ARG 0.005 0.000 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 2.018 Fit side-chains REVERT: A 537 LEU cc_start: 0.5728 (tp) cc_final: 0.5456 (tp) REVERT: B 433 MET cc_start: 0.5951 (ttm) cc_final: 0.5663 (ttm) REVERT: B 537 LEU cc_start: 0.5734 (tp) cc_final: 0.5459 (tp) REVERT: D 433 MET cc_start: 0.5951 (ttm) cc_final: 0.5660 (ttm) REVERT: D 537 LEU cc_start: 0.5736 (tp) cc_final: 0.5456 (tp) REVERT: C 433 MET cc_start: 0.5950 (ttm) cc_final: 0.5661 (ttm) REVERT: C 537 LEU cc_start: 0.5729 (tp) cc_final: 0.5456 (tp) outliers start: 37 outliers final: 24 residues processed: 189 average time/residue: 0.2580 time to fit residues: 80.1955 Evaluate side-chains 160 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 158 optimal weight: 50.0000 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17656 Z= 0.277 Angle : 0.766 13.404 24012 Z= 0.388 Chirality : 0.042 0.159 2764 Planarity : 0.005 0.037 2984 Dihedral : 6.493 33.957 2392 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.59 % Allowed : 15.63 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.62 (0.17), residues: 2196 helix: -0.14 (0.14), residues: 1284 sheet: -2.31 (0.63), residues: 56 loop : -2.43 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 677 HIS 0.007 0.002 HIS C 165 PHE 0.021 0.002 PHE A 207 TYR 0.024 0.002 TYR D 525 ARG 0.004 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 2.143 Fit side-chains REVERT: A 607 MET cc_start: 0.4359 (pmm) cc_final: 0.2547 (mpp) REVERT: A 640 MET cc_start: 0.7620 (tpt) cc_final: 0.7295 (tpt) REVERT: B 433 MET cc_start: 0.5855 (ttm) cc_final: 0.5501 (ttm) REVERT: B 607 MET cc_start: 0.4355 (pmm) cc_final: 0.2535 (mpp) REVERT: B 640 MET cc_start: 0.7608 (tpt) cc_final: 0.7259 (tpt) REVERT: D 433 MET cc_start: 0.5854 (ttm) cc_final: 0.5497 (ttm) REVERT: D 607 MET cc_start: 0.4179 (pmm) cc_final: 0.2372 (mpp) REVERT: D 640 MET cc_start: 0.7612 (tpt) cc_final: 0.7276 (tpt) REVERT: C 433 MET cc_start: 0.5855 (ttm) cc_final: 0.5499 (ttm) REVERT: C 607 MET cc_start: 0.4358 (pmm) cc_final: 0.2535 (mpp) REVERT: C 640 MET cc_start: 0.7607 (tpt) cc_final: 0.7272 (tpt) outliers start: 45 outliers final: 29 residues processed: 176 average time/residue: 0.2603 time to fit residues: 72.3757 Evaluate side-chains 142 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 0.0370 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 GLN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17656 Z= 0.174 Angle : 0.697 14.837 24012 Z= 0.345 Chirality : 0.039 0.145 2764 Planarity : 0.004 0.037 2984 Dihedral : 6.058 34.186 2392 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.18 % Allowed : 15.75 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.24 (0.18), residues: 2196 helix: 0.14 (0.14), residues: 1276 sheet: None (None), residues: 0 loop : -2.24 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 677 HIS 0.003 0.001 HIS A 165 PHE 0.012 0.001 PHE B 199 TYR 0.027 0.001 TYR D 525 ARG 0.003 0.000 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 2.045 Fit side-chains REVERT: A 607 MET cc_start: 0.3898 (pmm) cc_final: 0.2117 (mpp) REVERT: B 433 MET cc_start: 0.5963 (ttm) cc_final: 0.5666 (ttp) REVERT: B 607 MET cc_start: 0.3906 (pmm) cc_final: 0.2113 (mpp) REVERT: B 640 MET cc_start: 0.7589 (tpt) cc_final: 0.7362 (tpt) REVERT: D 433 MET cc_start: 0.5959 (ttm) cc_final: 0.5661 (ttp) REVERT: D 607 MET cc_start: 0.3879 (pmm) cc_final: 0.2124 (mpp) REVERT: D 640 MET cc_start: 0.7599 (tpt) cc_final: 0.7372 (tpt) REVERT: C 433 MET cc_start: 0.5962 (ttm) cc_final: 0.5665 (ttp) REVERT: C 607 MET cc_start: 0.3904 (pmm) cc_final: 0.2113 (mpp) REVERT: C 640 MET cc_start: 0.7595 (tpt) cc_final: 0.7369 (tpt) outliers start: 38 outliers final: 31 residues processed: 166 average time/residue: 0.2689 time to fit residues: 70.3236 Evaluate side-chains 156 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17656 Z= 0.241 Angle : 0.735 14.403 24012 Z= 0.372 Chirality : 0.043 0.317 2764 Planarity : 0.004 0.035 2984 Dihedral : 6.201 33.376 2392 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.64 % Allowed : 16.95 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.31 (0.18), residues: 2196 helix: 0.03 (0.14), residues: 1276 sheet: None (None), residues: 0 loop : -2.17 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 677 HIS 0.005 0.001 HIS A 165 PHE 0.018 0.002 PHE B 207 TYR 0.028 0.002 TYR D 525 ARG 0.003 0.000 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 120 time to evaluate : 2.005 Fit side-chains REVERT: B 433 MET cc_start: 0.5865 (ttm) cc_final: 0.5541 (ttp) REVERT: B 640 MET cc_start: 0.7649 (tpt) cc_final: 0.7364 (tpt) REVERT: D 433 MET cc_start: 0.5867 (ttm) cc_final: 0.5544 (ttp) REVERT: D 640 MET cc_start: 0.7654 (tpt) cc_final: 0.7370 (tpt) REVERT: C 433 MET cc_start: 0.5863 (ttm) cc_final: 0.5540 (ttp) REVERT: C 640 MET cc_start: 0.7652 (tpt) cc_final: 0.7367 (tpt) outliers start: 46 outliers final: 34 residues processed: 162 average time/residue: 0.2701 time to fit residues: 68.6453 Evaluate side-chains 158 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17656 Z= 0.217 Angle : 0.723 14.893 24012 Z= 0.363 Chirality : 0.042 0.249 2764 Planarity : 0.004 0.035 2984 Dihedral : 6.076 32.935 2392 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.36 % Allowed : 16.61 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.23 (0.18), residues: 2196 helix: 0.07 (0.14), residues: 1276 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.004 0.001 HIS A 165 PHE 0.015 0.001 PHE A 207 TYR 0.031 0.002 TYR D 525 ARG 0.003 0.000 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 2.146 Fit side-chains REVERT: A 492 MET cc_start: 0.7945 (ppp) cc_final: 0.7376 (ppp) REVERT: A 607 MET cc_start: 0.3820 (pmm) cc_final: 0.2387 (mpp) REVERT: B 433 MET cc_start: 0.5813 (ttm) cc_final: 0.5471 (ttp) REVERT: B 492 MET cc_start: 0.7951 (ppp) cc_final: 0.7381 (ppp) REVERT: B 607 MET cc_start: 0.3819 (pmm) cc_final: 0.2088 (mpp) REVERT: B 640 MET cc_start: 0.7601 (tpt) cc_final: 0.7373 (tpt) REVERT: D 433 MET cc_start: 0.5817 (ttm) cc_final: 0.5476 (ttp) REVERT: D 492 MET cc_start: 0.7951 (ppp) cc_final: 0.7384 (ppp) REVERT: D 640 MET cc_start: 0.7603 (tpt) cc_final: 0.7375 (tpt) REVERT: C 433 MET cc_start: 0.5813 (ttm) cc_final: 0.5472 (ttp) REVERT: C 492 MET cc_start: 0.7951 (ppp) cc_final: 0.7381 (ppp) REVERT: C 607 MET cc_start: 0.3771 (pmm) cc_final: 0.2012 (mpp) REVERT: C 640 MET cc_start: 0.7604 (tpt) cc_final: 0.7381 (tpt) outliers start: 41 outliers final: 37 residues processed: 177 average time/residue: 0.2601 time to fit residues: 73.0326 Evaluate side-chains 160 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 186 optimal weight: 0.1980 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17656 Z= 0.150 Angle : 0.702 15.577 24012 Z= 0.342 Chirality : 0.042 0.230 2764 Planarity : 0.004 0.038 2984 Dihedral : 5.554 33.464 2392 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.53 % Allowed : 17.13 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.87 (0.18), residues: 2196 helix: 0.39 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -2.00 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 676 HIS 0.002 0.000 HIS B 251 PHE 0.011 0.001 PHE C 199 TYR 0.028 0.001 TYR D 525 ARG 0.003 0.000 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.946 Fit side-chains REVERT: A 130 ASP cc_start: 0.7497 (t0) cc_final: 0.7012 (t0) REVERT: A 372 MET cc_start: 0.6830 (mmm) cc_final: 0.6385 (mmp) REVERT: A 433 MET cc_start: 0.6248 (ttm) cc_final: 0.5935 (ttp) REVERT: A 524 ILE cc_start: 0.6807 (mp) cc_final: 0.6535 (pt) REVERT: A 607 MET cc_start: 0.3684 (pmm) cc_final: 0.1409 (mpp) REVERT: B 130 ASP cc_start: 0.7375 (t0) cc_final: 0.6882 (t0) REVERT: B 433 MET cc_start: 0.6214 (ttm) cc_final: 0.5948 (ttp) REVERT: B 524 ILE cc_start: 0.6800 (mp) cc_final: 0.6532 (pt) REVERT: B 607 MET cc_start: 0.3689 (pmm) cc_final: 0.1038 (mpp) REVERT: D 130 ASP cc_start: 0.7374 (t0) cc_final: 0.6885 (t0) REVERT: D 433 MET cc_start: 0.6219 (ttm) cc_final: 0.5952 (ttp) REVERT: D 607 MET cc_start: 0.3359 (pmm) cc_final: 0.1584 (mpp) REVERT: C 130 ASP cc_start: 0.7376 (t0) cc_final: 0.6883 (t0) REVERT: C 433 MET cc_start: 0.6216 (ttm) cc_final: 0.5948 (ttp) REVERT: C 524 ILE cc_start: 0.6803 (mp) cc_final: 0.6536 (pt) REVERT: C 607 MET cc_start: 0.3617 (pmm) cc_final: 0.1400 (mpp) outliers start: 44 outliers final: 39 residues processed: 182 average time/residue: 0.2824 time to fit residues: 78.8491 Evaluate side-chains 169 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 676 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 676 TRP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 676 TRP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 676 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 134 optimal weight: 0.0770 chunk 107 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17656 Z= 0.197 Angle : 0.729 14.753 24012 Z= 0.360 Chirality : 0.042 0.219 2764 Planarity : 0.004 0.037 2984 Dihedral : 5.648 31.535 2392 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.36 % Allowed : 17.87 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.96 (0.18), residues: 2196 helix: 0.29 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -1.99 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 677 HIS 0.003 0.001 HIS C 165 PHE 0.015 0.001 PHE B 207 TYR 0.030 0.002 TYR B 525 ARG 0.002 0.000 ARG C 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 2.192 Fit side-chains REVERT: A 433 MET cc_start: 0.6001 (ttm) cc_final: 0.5651 (ttp) REVERT: A 492 MET cc_start: 0.7949 (ppp) cc_final: 0.7361 (ppp) REVERT: A 528 MET cc_start: 0.7238 (ppp) cc_final: 0.6827 (pmm) REVERT: A 607 MET cc_start: 0.3837 (pmm) cc_final: 0.1379 (mpp) REVERT: B 372 MET cc_start: 0.6195 (mmm) cc_final: 0.5517 (mmp) REVERT: B 433 MET cc_start: 0.5817 (ttm) cc_final: 0.5486 (ttp) REVERT: B 492 MET cc_start: 0.7951 (ppp) cc_final: 0.7363 (ppp) REVERT: B 528 MET cc_start: 0.7242 (ppp) cc_final: 0.6820 (pmm) REVERT: B 607 MET cc_start: 0.3842 (pmm) cc_final: 0.1762 (mpp) REVERT: D 433 MET cc_start: 0.5889 (ttm) cc_final: 0.5578 (ttp) REVERT: D 492 MET cc_start: 0.7946 (ppp) cc_final: 0.7356 (ppp) REVERT: D 607 MET cc_start: 0.3662 (pmm) cc_final: 0.1359 (mpp) REVERT: C 433 MET cc_start: 0.5818 (ttm) cc_final: 0.5489 (ttp) REVERT: C 492 MET cc_start: 0.7954 (ppp) cc_final: 0.7367 (ppp) REVERT: C 528 MET cc_start: 0.7241 (ppp) cc_final: 0.6815 (pmm) REVERT: C 607 MET cc_start: 0.3432 (pmm) cc_final: 0.1244 (mpp) outliers start: 41 outliers final: 40 residues processed: 174 average time/residue: 0.2682 time to fit residues: 74.2594 Evaluate side-chains 162 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 122 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 676 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 676 TRP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 676 TRP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 676 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 48 optimal weight: 40.0000 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.110624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.103782 restraints weight = 80100.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.104860 restraints weight = 55146.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.105711 restraints weight = 41023.295| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17656 Z= 0.165 Angle : 0.720 15.747 24012 Z= 0.347 Chirality : 0.042 0.210 2764 Planarity : 0.004 0.038 2984 Dihedral : 5.494 31.321 2392 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.53 % Allowed : 18.22 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.65 (0.18), residues: 2196 helix: 0.55 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -1.81 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 386 HIS 0.002 0.001 HIS A 165 PHE 0.012 0.001 PHE C 199 TYR 0.034 0.001 TYR B 525 ARG 0.003 0.000 ARG D 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.48 seconds wall clock time: 52 minutes 3.75 seconds (3123.75 seconds total)