Starting phenix.real_space_refine on Fri Jun 13 21:13:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smk_40589/06_2025/8smk_40589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smk_40589/06_2025/8smk_40589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8smk_40589/06_2025/8smk_40589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smk_40589/06_2025/8smk_40589.map" model { file = "/net/cci-nas-00/data/ceres_data/8smk_40589/06_2025/8smk_40589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smk_40589/06_2025/8smk_40589.cif" } resolution = 3.5 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= 0.014 sd= 0.387 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 82 5.16 5 C 9712 2.51 5 N 2556 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4348 Classifications: {'peptide': 555} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 520} Chain breaks: 10 Chain: "B" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1653 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain: "C" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1644 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: D, F, E Time building chain proxies: 12.04, per 1000 atoms: 0.79 Number of scatterers: 15298 At special positions: 0 Unit cell: (139.445, 181.195, 105.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 82 16.00 O 2940 8.00 N 2556 7.00 C 9712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.16 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.16 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 44 sheets defined 15.3% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 557 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 320 through 330 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 526 through 531 Processing helix chain 'D' and resid 532 through 557 Processing helix chain 'D' and resid 560 through 562 No H-bonds generated for 'chain 'D' and resid 560 through 562' Processing helix chain 'D' and resid 611 through 621 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 7.226A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.312A pdb=" N VAL A 283 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP A 273 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 285 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 removed outlier: 8.740A pdb=" N GLY A 390 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL A 392 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 367 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 335 removed outlier: 7.049A pdb=" N GLN A 306 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A 335 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 308 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AB3, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.712A pdb=" N ILE B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.146A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.146A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 115 through 119 removed outlier: 4.991A pdb=" N SER C 132 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU C 182 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL C 134 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU C 180 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU C 136 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 178 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN C 138 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 176 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 155 removed outlier: 4.069A pdb=" N ALA C 194 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 8 removed outlier: 7.226A pdb=" N ILE D 7 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR D 15 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR D 111 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 17 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 113 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS D 19 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 115 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR D 15 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR D 111 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 17 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 113 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS D 19 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 115 " --> pdb=" O CYS D 19 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL D 213 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.312A pdb=" N VAL D 283 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP D 273 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 285 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU D 199 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.740A pdb=" N GLY D 390 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL D 392 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 367 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 333 through 335 removed outlier: 7.048A pdb=" N GLN D 306 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR D 335 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 308 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AD3, first strand: chain 'D' and resid 416 through 418 Processing sheet with id=AD4, first strand: chain 'D' and resid 476 through 480 Processing sheet with id=AD5, first strand: chain 'D' and resid 571 through 573 Processing sheet with id=AD6, first strand: chain 'D' and resid 590 through 592 Processing sheet with id=AD7, first strand: chain 'D' and resid 605 through 606 Processing sheet with id=AD8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.712A pdb=" N ILE E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 128 through 132 removed outlier: 6.146A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 139 through 140 removed outlier: 6.146A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 159 through 162 Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.991A pdb=" N SER F 132 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU F 182 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU F 180 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU F 136 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER F 178 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU F 176 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 154 through 155 removed outlier: 4.068A pdb=" N ALA F 194 " --> pdb=" O LYS F 150 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1488 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: 5.98 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2690 1.32 - 1.44: 4017 1.44 - 1.56: 8807 1.56 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15630 Sorted by residual: bond pdb=" N PRO F 8 " pdb=" CD PRO F 8 " ideal model delta sigma weight residual 1.474 1.405 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" N PRO C 8 " pdb=" CD PRO C 8 " ideal model delta sigma weight residual 1.474 1.405 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" N PRO A 480 " pdb=" CD PRO A 480 " ideal model delta sigma weight residual 1.473 1.411 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" N PRO D 480 " pdb=" CD PRO D 480 " ideal model delta sigma weight residual 1.473 1.411 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" N PRO D 436 " pdb=" CD PRO D 436 " ideal model delta sigma weight residual 1.473 1.413 0.060 1.40e-02 5.10e+03 1.87e+01 ... (remaining 15625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 17590 1.78 - 3.56: 3111 3.56 - 5.34: 453 5.34 - 7.12: 46 7.12 - 8.90: 12 Bond angle restraints: 21212 Sorted by residual: angle pdb=" N ALA A 119 " pdb=" CA ALA A 119 " pdb=" C ALA A 119 " ideal model delta sigma weight residual 111.74 120.64 -8.90 1.35e+00 5.49e-01 4.34e+01 angle pdb=" N ALA D 119 " pdb=" CA ALA D 119 " pdb=" C ALA D 119 " ideal model delta sigma weight residual 111.74 120.64 -8.90 1.35e+00 5.49e-01 4.34e+01 angle pdb=" C PRO F 142 " pdb=" N ARG F 143 " pdb=" CA ARG F 143 " ideal model delta sigma weight residual 120.28 128.11 -7.83 1.34e+00 5.57e-01 3.41e+01 angle pdb=" C PRO C 142 " pdb=" N ARG C 143 " pdb=" CA ARG C 143 " ideal model delta sigma weight residual 120.28 128.08 -7.80 1.34e+00 5.57e-01 3.38e+01 angle pdb=" C PHE D 261 " pdb=" N PRO D 262 " pdb=" CA PRO D 262 " ideal model delta sigma weight residual 119.56 125.13 -5.57 1.02e+00 9.61e-01 2.99e+01 ... (remaining 21207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 9046 16.99 - 33.98: 222 33.98 - 50.97: 50 50.97 - 67.95: 50 67.95 - 84.94: 18 Dihedral angle restraints: 9386 sinusoidal: 3662 harmonic: 5724 Sorted by residual: dihedral pdb=" C ARG A 123 " pdb=" N ARG A 123 " pdb=" CA ARG A 123 " pdb=" CB ARG A 123 " ideal model delta harmonic sigma weight residual -122.60 -131.66 9.06 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" C ARG D 123 " pdb=" N ARG D 123 " pdb=" CA ARG D 123 " pdb=" CB ARG D 123 " ideal model delta harmonic sigma weight residual -122.60 -131.66 9.06 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" CA SER A 413 " pdb=" C SER A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1747 0.064 - 0.129: 472 0.129 - 0.193: 181 0.193 - 0.258: 8 0.258 - 0.322: 2 Chirality restraints: 2410 Sorted by residual: chirality pdb=" CA ARG D 123 " pdb=" N ARG D 123 " pdb=" C ARG D 123 " pdb=" CB ARG D 123 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ARG A 123 " pdb=" N ARG A 123 " pdb=" C ARG A 123 " pdb=" CB ARG A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ALA D 119 " pdb=" N ALA D 119 " pdb=" C ALA D 119 " pdb=" CB ALA D 119 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2407 not shown) Planarity restraints: 2704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 105 " 0.107 2.00e-02 2.50e+03 5.40e-02 5.83e+01 pdb=" CG TYR E 105 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR E 105 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR E 105 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR E 105 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 105 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 105 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 105 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " -0.107 2.00e-02 2.50e+03 5.40e-02 5.82e+01 pdb=" CG TYR B 105 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 94 " -0.045 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR B 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 94 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 94 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 94 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR B 94 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 94 " -0.062 2.00e-02 2.50e+03 ... (remaining 2701 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 65 2.62 - 3.19: 12539 3.19 - 3.76: 22358 3.76 - 4.33: 32705 4.33 - 4.90: 53252 Nonbonded interactions: 120919 Sorted by model distance: nonbonded pdb=" OD1 ASP A 168 " pdb="CA CA A 704 " model vdw 2.054 2.510 nonbonded pdb=" OD1 ASP D 168 " pdb="CA CA D 704 " model vdw 2.054 2.510 nonbonded pdb=" OD2 ASP D 157 " pdb="CA CA D 702 " model vdw 2.096 2.510 nonbonded pdb=" OD2 ASP A 157 " pdb="CA CA A 702 " model vdw 2.096 2.510 nonbonded pdb=" OD1 ASP D 155 " pdb="CA CA D 702 " model vdw 2.115 2.510 ... (remaining 120914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 17.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 61.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.011 0.127 15634 Z= 0.746 Angle : 1.377 8.897 21220 Z= 0.958 Chirality : 0.064 0.322 2410 Planarity : 0.008 0.083 2704 Dihedral : 11.016 84.943 5678 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1930 helix: 0.55 (0.36), residues: 180 sheet: 1.12 (0.19), residues: 690 loop : 0.86 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP A 466 HIS 0.002 0.000 HIS C 199 PHE 0.039 0.003 PHE D 487 TYR 0.107 0.003 TYR E 105 ARG 0.009 0.001 ARG D 427 Details of bonding type rmsd hydrogen bonds : bond 0.19103 ( 592) hydrogen bonds : angle 7.94756 ( 1488) SS BOND : bond 0.08971 ( 4) SS BOND : angle 2.72888 ( 8) covalent geometry : bond 0.01136 (15630) covalent geometry : angle 1.37648 (21212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8038 (mt) cc_final: 0.7801 (pt) REVERT: A 184 THR cc_start: 0.8525 (m) cc_final: 0.8032 (p) REVERT: A 188 LYS cc_start: 0.7566 (tttt) cc_final: 0.6967 (tttt) REVERT: A 196 ASN cc_start: 0.7803 (m-40) cc_final: 0.7225 (p0) REVERT: A 244 LYS cc_start: 0.8542 (tptt) cc_final: 0.7769 (tptt) REVERT: A 502 GLN cc_start: 0.7073 (tp40) cc_final: 0.6773 (mm110) REVERT: A 527 LYS cc_start: 0.6746 (pttt) cc_final: 0.6389 (mtpp) REVERT: B 77 ASN cc_start: 0.8409 (t0) cc_final: 0.7883 (t0) REVERT: B 186 LEU cc_start: 0.8419 (pp) cc_final: 0.8133 (pp) REVERT: C 61 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7195 (mtp180) REVERT: C 77 SER cc_start: 0.7998 (m) cc_final: 0.7243 (t) REVERT: C 79 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7326 (mp10) REVERT: C 83 PHE cc_start: 0.8410 (m-80) cc_final: 0.8184 (m-80) REVERT: C 177 SER cc_start: 0.8305 (t) cc_final: 0.7670 (p) REVERT: C 178 SER cc_start: 0.8087 (t) cc_final: 0.7767 (p) REVERT: D 24 LEU cc_start: 0.8043 (mt) cc_final: 0.7802 (pt) REVERT: D 184 THR cc_start: 0.8520 (m) cc_final: 0.8025 (p) REVERT: D 188 LYS cc_start: 0.7562 (tttt) cc_final: 0.6953 (tttt) REVERT: D 196 ASN cc_start: 0.7799 (m-40) cc_final: 0.7226 (p0) REVERT: D 244 LYS cc_start: 0.8539 (tptt) cc_final: 0.7774 (tptt) REVERT: D 502 GLN cc_start: 0.7075 (tp40) cc_final: 0.6778 (mm110) REVERT: D 527 LYS cc_start: 0.6747 (pttt) cc_final: 0.6390 (mtpp) REVERT: E 77 ASN cc_start: 0.8400 (t0) cc_final: 0.7874 (t0) REVERT: E 186 LEU cc_start: 0.8411 (pp) cc_final: 0.8127 (pp) REVERT: F 61 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7200 (mtp180) REVERT: F 77 SER cc_start: 0.7996 (m) cc_final: 0.7237 (t) REVERT: F 79 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7316 (mp10) REVERT: F 83 PHE cc_start: 0.8411 (m-80) cc_final: 0.8188 (m-80) REVERT: F 177 SER cc_start: 0.8311 (t) cc_final: 0.7878 (p) REVERT: F 178 SER cc_start: 0.8078 (t) cc_final: 0.7861 (p) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3211 time to fit residues: 208.5774 Evaluate side-chains 270 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.0050 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 471 HIS ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 471 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.178806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131217 restraints weight = 22987.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134115 restraints weight = 11878.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136262 restraints weight = 7781.535| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15634 Z= 0.130 Angle : 0.577 6.783 21220 Z= 0.304 Chirality : 0.045 0.145 2410 Planarity : 0.005 0.055 2704 Dihedral : 4.398 17.701 2100 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.62 % Allowed : 7.69 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.20), residues: 1930 helix: 1.90 (0.38), residues: 182 sheet: 1.34 (0.19), residues: 762 loop : 1.04 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 141 HIS 0.005 0.001 HIS D 245 PHE 0.016 0.001 PHE A 407 TYR 0.018 0.002 TYR F 141 ARG 0.003 0.001 ARG D 484 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 592) hydrogen bonds : angle 5.33339 ( 1488) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.88484 ( 8) covalent geometry : bond 0.00296 (15630) covalent geometry : angle 0.57636 (21212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 294 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 188 LYS cc_start: 0.7626 (tttt) cc_final: 0.7228 (tttt) REVERT: A 193 PHE cc_start: 0.9097 (t80) cc_final: 0.8721 (t80) REVERT: A 196 ASN cc_start: 0.8049 (m-40) cc_final: 0.7462 (p0) REVERT: A 244 LYS cc_start: 0.8500 (tptt) cc_final: 0.7507 (tptt) REVERT: A 247 MET cc_start: 0.8017 (tpt) cc_final: 0.7809 (tpt) REVERT: A 276 ASN cc_start: 0.8338 (t0) cc_final: 0.7901 (t0) REVERT: A 352 MET cc_start: 0.7514 (mtt) cc_final: 0.7246 (mtt) REVERT: A 407 PHE cc_start: 0.7573 (m-10) cc_final: 0.7253 (m-80) REVERT: A 474 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7853 (mt-10) REVERT: A 527 LYS cc_start: 0.7024 (pttt) cc_final: 0.6415 (mtpp) REVERT: A 554 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8441 (mtpt) REVERT: B 77 ASN cc_start: 0.8570 (t0) cc_final: 0.8191 (t0) REVERT: C 22 THR cc_start: 0.8585 (p) cc_final: 0.8347 (t) REVERT: C 140 PHE cc_start: 0.8253 (p90) cc_final: 0.7798 (p90) REVERT: C 167 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 45 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8345 (m) REVERT: D 188 LYS cc_start: 0.7625 (tttt) cc_final: 0.7228 (tttt) REVERT: D 193 PHE cc_start: 0.9099 (t80) cc_final: 0.8722 (t80) REVERT: D 196 ASN cc_start: 0.8041 (m-40) cc_final: 0.7458 (p0) REVERT: D 244 LYS cc_start: 0.8500 (tptt) cc_final: 0.7510 (tptt) REVERT: D 276 ASN cc_start: 0.8337 (t0) cc_final: 0.7903 (t0) REVERT: D 352 MET cc_start: 0.7511 (mtt) cc_final: 0.7241 (mtt) REVERT: D 407 PHE cc_start: 0.7573 (m-10) cc_final: 0.7251 (m-80) REVERT: D 474 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7849 (mt-10) REVERT: D 527 LYS cc_start: 0.7021 (pttt) cc_final: 0.6414 (mtpp) REVERT: D 554 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8440 (mtpt) REVERT: E 77 ASN cc_start: 0.8568 (t0) cc_final: 0.8192 (t0) REVERT: F 22 THR cc_start: 0.8585 (p) cc_final: 0.8346 (t) REVERT: F 140 PHE cc_start: 0.8264 (p90) cc_final: 0.7785 (p90) REVERT: F 167 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7838 (tm-30) REVERT: F 177 SER cc_start: 0.8148 (t) cc_final: 0.7807 (p) REVERT: F 178 SER cc_start: 0.8222 (t) cc_final: 0.8002 (p) outliers start: 28 outliers final: 16 residues processed: 310 average time/residue: 0.2947 time to fit residues: 132.1694 Evaluate side-chains 243 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 0.0370 chunk 137 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.171189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123896 restraints weight = 23162.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127122 restraints weight = 11741.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127966 restraints weight = 7965.845| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15634 Z= 0.183 Angle : 0.585 8.786 21220 Z= 0.304 Chirality : 0.045 0.155 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.349 18.447 2100 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.77 % Allowed : 9.60 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1930 helix: 1.81 (0.39), residues: 184 sheet: 1.22 (0.19), residues: 782 loop : 0.73 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 141 HIS 0.005 0.001 HIS A 236 PHE 0.016 0.002 PHE D 583 TYR 0.022 0.002 TYR B 153 ARG 0.004 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 592) hydrogen bonds : angle 5.08086 ( 1488) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.68290 ( 8) covalent geometry : bond 0.00441 (15630) covalent geometry : angle 0.58531 (21212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: A 193 PHE cc_start: 0.9160 (t80) cc_final: 0.8766 (t80) REVERT: A 196 ASN cc_start: 0.8193 (m-40) cc_final: 0.7568 (p0) REVERT: A 464 SER cc_start: 0.9237 (p) cc_final: 0.8925 (t) REVERT: A 527 LYS cc_start: 0.7115 (pttt) cc_final: 0.6498 (mtpp) REVERT: A 543 GLU cc_start: 0.7914 (tt0) cc_final: 0.7655 (tt0) REVERT: A 554 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8616 (mtpt) REVERT: B 77 ASN cc_start: 0.8550 (t0) cc_final: 0.8198 (t0) REVERT: C 22 THR cc_start: 0.8604 (p) cc_final: 0.8360 (t) REVERT: C 167 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7841 (tm-30) REVERT: D 183 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7882 (ttp) REVERT: D 193 PHE cc_start: 0.9164 (t80) cc_final: 0.8772 (t80) REVERT: D 196 ASN cc_start: 0.8197 (m-40) cc_final: 0.7577 (p0) REVERT: D 464 SER cc_start: 0.9243 (p) cc_final: 0.8896 (t) REVERT: D 527 LYS cc_start: 0.7118 (pttt) cc_final: 0.6500 (mtpp) REVERT: D 543 GLU cc_start: 0.7900 (tt0) cc_final: 0.7644 (tt0) REVERT: D 554 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (mtpt) REVERT: E 77 ASN cc_start: 0.8551 (t0) cc_final: 0.8198 (t0) REVERT: F 22 THR cc_start: 0.8605 (p) cc_final: 0.8358 (t) outliers start: 48 outliers final: 29 residues processed: 256 average time/residue: 0.3361 time to fit residues: 124.4426 Evaluate side-chains 232 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.171362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121141 restraints weight = 23075.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124998 restraints weight = 12480.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127560 restraints weight = 8559.820| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15634 Z= 0.151 Angle : 0.558 7.966 21220 Z= 0.286 Chirality : 0.044 0.185 2410 Planarity : 0.005 0.044 2704 Dihedral : 4.207 17.163 2100 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.49 % Allowed : 9.94 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1930 helix: 1.54 (0.38), residues: 198 sheet: 1.39 (0.19), residues: 792 loop : 0.60 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 139 HIS 0.004 0.001 HIS A 245 PHE 0.013 0.001 PHE D 583 TYR 0.016 0.001 TYR F 49 ARG 0.004 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 592) hydrogen bonds : angle 4.82033 ( 1488) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.62877 ( 8) covalent geometry : bond 0.00362 (15630) covalent geometry : angle 0.55821 (21212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9119 (t80) cc_final: 0.8686 (t80) REVERT: A 196 ASN cc_start: 0.8230 (m-40) cc_final: 0.7668 (p0) REVERT: A 464 SER cc_start: 0.9237 (p) cc_final: 0.8875 (t) REVERT: A 527 LYS cc_start: 0.7374 (pttt) cc_final: 0.6753 (mtpp) REVERT: B 77 ASN cc_start: 0.8591 (t0) cc_final: 0.7902 (t0) REVERT: C 22 THR cc_start: 0.8612 (p) cc_final: 0.8398 (t) REVERT: D 193 PHE cc_start: 0.9121 (t80) cc_final: 0.8686 (t80) REVERT: D 196 ASN cc_start: 0.8229 (m-40) cc_final: 0.7669 (p0) REVERT: D 464 SER cc_start: 0.9240 (p) cc_final: 0.8846 (t) REVERT: D 527 LYS cc_start: 0.7371 (pttt) cc_final: 0.6755 (mtpp) REVERT: E 77 ASN cc_start: 0.8590 (t0) cc_final: 0.7905 (t0) REVERT: F 22 THR cc_start: 0.8609 (p) cc_final: 0.8395 (t) outliers start: 43 outliers final: 25 residues processed: 249 average time/residue: 0.3073 time to fit residues: 109.4718 Evaluate side-chains 220 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 6 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 135 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN F 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119572 restraints weight = 23346.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122796 restraints weight = 11853.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123689 restraints weight = 8117.153| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15634 Z= 0.207 Angle : 0.597 9.285 21220 Z= 0.309 Chirality : 0.045 0.192 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.455 18.412 2100 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.89 % Allowed : 10.58 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1930 helix: 1.22 (0.37), residues: 202 sheet: 1.18 (0.18), residues: 808 loop : 0.33 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 141 HIS 0.005 0.001 HIS D 236 PHE 0.017 0.002 PHE A 583 TYR 0.019 0.002 TYR C 49 ARG 0.004 0.001 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 592) hydrogen bonds : angle 4.93850 ( 1488) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.64898 ( 8) covalent geometry : bond 0.00501 (15630) covalent geometry : angle 0.59704 (21212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8310 (m-40) cc_final: 0.7790 (p0) REVERT: A 464 SER cc_start: 0.9251 (p) cc_final: 0.8914 (t) REVERT: A 527 LYS cc_start: 0.7413 (pttt) cc_final: 0.6791 (mtpp) REVERT: A 576 PHE cc_start: 0.7424 (m-80) cc_final: 0.7068 (t80) REVERT: B 77 ASN cc_start: 0.8614 (t0) cc_final: 0.8031 (t0) REVERT: C 22 THR cc_start: 0.8660 (p) cc_final: 0.8416 (t) REVERT: C 42 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8552 (mttp) REVERT: D 196 ASN cc_start: 0.8309 (m-40) cc_final: 0.7785 (p0) REVERT: D 464 SER cc_start: 0.9252 (p) cc_final: 0.8888 (t) REVERT: D 527 LYS cc_start: 0.7415 (pttt) cc_final: 0.6794 (mtpp) REVERT: D 576 PHE cc_start: 0.7422 (m-80) cc_final: 0.7068 (t80) REVERT: E 77 ASN cc_start: 0.8612 (t0) cc_final: 0.8027 (t0) REVERT: F 22 THR cc_start: 0.8658 (p) cc_final: 0.8418 (t) REVERT: F 42 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8550 (mttp) outliers start: 50 outliers final: 33 residues processed: 244 average time/residue: 0.3022 time to fit residues: 106.4976 Evaluate side-chains 234 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 0.0970 chunk 175 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.170007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120176 restraints weight = 23259.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123973 restraints weight = 12466.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126476 restraints weight = 8513.848| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15634 Z= 0.126 Angle : 0.539 8.175 21220 Z= 0.275 Chirality : 0.043 0.184 2410 Planarity : 0.005 0.046 2704 Dihedral : 4.127 16.563 2100 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.14 % Allowed : 10.69 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1930 helix: 1.42 (0.37), residues: 204 sheet: 1.31 (0.18), residues: 796 loop : 0.34 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 35 HIS 0.003 0.001 HIS A 236 PHE 0.009 0.001 PHE D 583 TYR 0.014 0.001 TYR F 49 ARG 0.004 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 592) hydrogen bonds : angle 4.70794 ( 1488) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.61543 ( 8) covalent geometry : bond 0.00301 (15630) covalent geometry : angle 0.53904 (21212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7916 (m-30) cc_final: 0.7527 (m-30) REVERT: A 193 PHE cc_start: 0.9000 (t80) cc_final: 0.8549 (t80) REVERT: A 196 ASN cc_start: 0.8211 (m-40) cc_final: 0.7665 (p0) REVERT: A 298 MET cc_start: 0.8795 (ttt) cc_final: 0.8558 (ttt) REVERT: A 461 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8137 (ttmt) REVERT: A 464 SER cc_start: 0.9244 (p) cc_final: 0.8945 (t) REVERT: A 527 LYS cc_start: 0.7390 (pttt) cc_final: 0.6788 (mtpp) REVERT: A 576 PHE cc_start: 0.7424 (m-80) cc_final: 0.7069 (t80) REVERT: B 77 ASN cc_start: 0.8569 (t0) cc_final: 0.7954 (t0) REVERT: C 42 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8549 (mttp) REVERT: D 173 ASP cc_start: 0.7940 (m-30) cc_final: 0.7547 (m-30) REVERT: D 193 PHE cc_start: 0.9002 (t80) cc_final: 0.8555 (t80) REVERT: D 196 ASN cc_start: 0.8210 (m-40) cc_final: 0.7660 (p0) REVERT: D 215 GLN cc_start: 0.7982 (tt0) cc_final: 0.7763 (tt0) REVERT: D 298 MET cc_start: 0.8792 (ttt) cc_final: 0.8563 (ttt) REVERT: D 461 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8144 (ttmt) REVERT: D 464 SER cc_start: 0.9252 (p) cc_final: 0.8908 (t) REVERT: D 527 LYS cc_start: 0.7390 (pttt) cc_final: 0.6790 (mtpp) REVERT: D 576 PHE cc_start: 0.7416 (m-80) cc_final: 0.7061 (t80) REVERT: E 77 ASN cc_start: 0.8577 (t0) cc_final: 0.7961 (t0) REVERT: F 42 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8544 (mttp) outliers start: 37 outliers final: 29 residues processed: 250 average time/residue: 0.2921 time to fit residues: 105.1146 Evaluate side-chains 235 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 34 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 137 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121552 restraints weight = 23309.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125409 restraints weight = 12370.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128022 restraints weight = 8419.902| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15634 Z= 0.115 Angle : 0.545 8.212 21220 Z= 0.275 Chirality : 0.043 0.184 2410 Planarity : 0.005 0.043 2704 Dihedral : 4.015 17.018 2100 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.31 % Allowed : 11.04 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1930 helix: 1.65 (0.38), residues: 204 sheet: 1.50 (0.19), residues: 778 loop : 0.34 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 35 HIS 0.003 0.001 HIS A 236 PHE 0.017 0.001 PHE A 40 TYR 0.013 0.001 TYR C 49 ARG 0.004 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 592) hydrogen bonds : angle 4.59638 ( 1488) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.46574 ( 8) covalent geometry : bond 0.00274 (15630) covalent geometry : angle 0.54518 (21212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8954 (t80) cc_final: 0.8380 (t80) REVERT: A 196 ASN cc_start: 0.8246 (m-40) cc_final: 0.7805 (p0) REVERT: A 464 SER cc_start: 0.9237 (p) cc_final: 0.8948 (t) REVERT: A 527 LYS cc_start: 0.7407 (pttt) cc_final: 0.6847 (mtpp) REVERT: A 576 PHE cc_start: 0.7415 (m-80) cc_final: 0.7068 (t80) REVERT: B 77 ASN cc_start: 0.8572 (t0) cc_final: 0.7925 (t0) REVERT: C 42 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8568 (mttp) REVERT: D 193 PHE cc_start: 0.8957 (t80) cc_final: 0.8382 (t80) REVERT: D 196 ASN cc_start: 0.8247 (m-40) cc_final: 0.7803 (p0) REVERT: D 464 SER cc_start: 0.9240 (p) cc_final: 0.8899 (t) REVERT: D 527 LYS cc_start: 0.7411 (pttt) cc_final: 0.6851 (mtpp) REVERT: D 576 PHE cc_start: 0.7406 (m-80) cc_final: 0.7061 (t80) REVERT: E 77 ASN cc_start: 0.8571 (t0) cc_final: 0.7935 (t0) REVERT: F 42 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8565 (mttp) outliers start: 40 outliers final: 29 residues processed: 232 average time/residue: 0.2901 time to fit residues: 98.6134 Evaluate side-chains 220 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 187 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120862 restraints weight = 23340.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123877 restraints weight = 11842.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124921 restraints weight = 7950.358| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15634 Z= 0.175 Angle : 0.572 9.184 21220 Z= 0.292 Chirality : 0.044 0.195 2410 Planarity : 0.005 0.044 2704 Dihedral : 4.235 17.479 2100 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.37 % Allowed : 12.14 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1930 helix: 1.70 (0.38), residues: 204 sheet: 1.39 (0.19), residues: 778 loop : 0.22 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 141 HIS 0.005 0.001 HIS D 236 PHE 0.014 0.001 PHE A 583 TYR 0.018 0.001 TYR C 49 ARG 0.003 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 592) hydrogen bonds : angle 4.70786 ( 1488) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.57890 ( 8) covalent geometry : bond 0.00427 (15630) covalent geometry : angle 0.57167 (21212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9072 (t80) cc_final: 0.8740 (t80) REVERT: A 196 ASN cc_start: 0.8309 (m-40) cc_final: 0.7813 (p0) REVERT: A 464 SER cc_start: 0.9255 (p) cc_final: 0.8968 (t) REVERT: A 527 LYS cc_start: 0.7339 (pttt) cc_final: 0.6769 (mtpp) REVERT: B 77 ASN cc_start: 0.8586 (t0) cc_final: 0.7968 (t0) REVERT: B 89 GLU cc_start: 0.8953 (pm20) cc_final: 0.8716 (pm20) REVERT: C 42 LYS cc_start: 0.8882 (mmtp) cc_final: 0.8555 (mttp) REVERT: D 193 PHE cc_start: 0.9071 (t80) cc_final: 0.8739 (t80) REVERT: D 196 ASN cc_start: 0.8309 (m-40) cc_final: 0.7806 (p0) REVERT: D 464 SER cc_start: 0.9257 (p) cc_final: 0.8926 (t) REVERT: D 527 LYS cc_start: 0.7348 (pttt) cc_final: 0.6784 (mtpp) REVERT: E 77 ASN cc_start: 0.8587 (t0) cc_final: 0.7973 (t0) REVERT: F 42 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8552 (mttp) outliers start: 41 outliers final: 33 residues processed: 223 average time/residue: 0.3046 time to fit residues: 98.3626 Evaluate side-chains 221 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.168582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118815 restraints weight = 23325.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122609 restraints weight = 12415.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125071 restraints weight = 8473.221| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15634 Z= 0.154 Angle : 0.561 8.819 21220 Z= 0.284 Chirality : 0.044 0.193 2410 Planarity : 0.005 0.044 2704 Dihedral : 4.211 16.856 2100 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.25 % Allowed : 12.14 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1930 helix: 1.67 (0.38), residues: 204 sheet: 1.39 (0.19), residues: 778 loop : 0.20 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.004 0.001 HIS D 236 PHE 0.019 0.001 PHE A 40 TYR 0.016 0.001 TYR C 49 ARG 0.002 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 592) hydrogen bonds : angle 4.67857 ( 1488) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.54384 ( 8) covalent geometry : bond 0.00374 (15630) covalent geometry : angle 0.56135 (21212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9048 (t80) cc_final: 0.8572 (t80) REVERT: A 196 ASN cc_start: 0.8314 (m-40) cc_final: 0.7896 (p0) REVERT: A 278 GLU cc_start: 0.8035 (pm20) cc_final: 0.7770 (pm20) REVERT: A 527 LYS cc_start: 0.7414 (pttt) cc_final: 0.6848 (mtpp) REVERT: B 77 ASN cc_start: 0.8588 (t0) cc_final: 0.8021 (t0) REVERT: B 89 GLU cc_start: 0.9002 (pm20) cc_final: 0.8765 (pm20) REVERT: C 42 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8581 (mttp) REVERT: D 193 PHE cc_start: 0.9048 (t80) cc_final: 0.8572 (t80) REVERT: D 196 ASN cc_start: 0.8315 (m-40) cc_final: 0.7896 (p0) REVERT: D 278 GLU cc_start: 0.8030 (pm20) cc_final: 0.7765 (pm20) REVERT: D 527 LYS cc_start: 0.7461 (pttt) cc_final: 0.6900 (mtpp) REVERT: E 77 ASN cc_start: 0.8589 (t0) cc_final: 0.8027 (t0) REVERT: F 42 LYS cc_start: 0.8840 (mmtp) cc_final: 0.8580 (mttp) outliers start: 39 outliers final: 34 residues processed: 217 average time/residue: 0.2896 time to fit residues: 92.1636 Evaluate side-chains 219 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 83 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 158 optimal weight: 0.0470 chunk 141 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123353 restraints weight = 23517.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126255 restraints weight = 11771.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127520 restraints weight = 7844.013| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15634 Z= 0.123 Angle : 0.542 8.536 21220 Z= 0.272 Chirality : 0.044 0.190 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.050 16.277 2100 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.14 % Allowed : 12.20 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1930 helix: 1.72 (0.38), residues: 204 sheet: 1.47 (0.19), residues: 778 loop : 0.25 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.003 0.001 HIS D 236 PHE 0.018 0.001 PHE A 40 TYR 0.014 0.001 TYR F 49 ARG 0.003 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 592) hydrogen bonds : angle 4.54960 ( 1488) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.51949 ( 8) covalent geometry : bond 0.00297 (15630) covalent geometry : angle 0.54225 (21212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8992 (t80) cc_final: 0.8499 (t80) REVERT: A 196 ASN cc_start: 0.8254 (m-40) cc_final: 0.7885 (p0) REVERT: A 527 LYS cc_start: 0.7387 (pttt) cc_final: 0.6838 (mtpp) REVERT: B 77 ASN cc_start: 0.8566 (t0) cc_final: 0.8174 (t0) REVERT: B 89 GLU cc_start: 0.8986 (pm20) cc_final: 0.8767 (pm20) REVERT: C 42 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8560 (mttp) REVERT: D 193 PHE cc_start: 0.8992 (t80) cc_final: 0.8498 (t80) REVERT: D 196 ASN cc_start: 0.8271 (m-40) cc_final: 0.7894 (p0) REVERT: D 527 LYS cc_start: 0.7398 (pttt) cc_final: 0.6962 (mtpp) REVERT: E 77 ASN cc_start: 0.8564 (t0) cc_final: 0.8173 (t0) REVERT: F 42 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8556 (mttp) outliers start: 37 outliers final: 32 residues processed: 217 average time/residue: 0.3001 time to fit residues: 95.5916 Evaluate side-chains 214 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 77 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.169483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123450 restraints weight = 23198.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125150 restraints weight = 11759.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126855 restraints weight = 8111.602| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15634 Z= 0.135 Angle : 0.549 8.732 21220 Z= 0.276 Chirality : 0.044 0.188 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.087 16.407 2100 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.02 % Allowed : 12.43 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1930 helix: 1.77 (0.38), residues: 204 sheet: 1.49 (0.19), residues: 778 loop : 0.23 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.004 0.001 HIS D 236 PHE 0.019 0.001 PHE D 40 TYR 0.015 0.001 TYR F 49 ARG 0.003 0.000 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 592) hydrogen bonds : angle 4.55735 ( 1488) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.51515 ( 8) covalent geometry : bond 0.00329 (15630) covalent geometry : angle 0.54936 (21212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5913.00 seconds wall clock time: 105 minutes 12.48 seconds (6312.48 seconds total)