Starting phenix.real_space_refine on Sat Aug 23 23:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smk_40589/08_2025/8smk_40589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smk_40589/08_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_40589/08_2025/8smk_40589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smk_40589/08_2025/8smk_40589.map" model { file = "/net/cci-nas-00/data/ceres_data/8smk_40589/08_2025/8smk_40589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smk_40589/08_2025/8smk_40589.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, E, F Time building chain proxies: 4.07, per 1000 atoms: 0.27 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: 0.85 Conformation dependent library (CDL) restraints added in 664.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.50 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: 2.07 Time building geometry restraints manager: 1.18 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 3.870 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG D 427 TYR 0.107 0.003 TYR E 105 PHE 0.039 0.003 PHE D 487 TRP 0.049 0.006 TRP A 466 HIS 0.002 0.000 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.01136 (15630) covalent geometry : angle 1.37648 (21212) SS BOND : bond 0.08971 ( 4) SS BOND : angle 2.72888 ( 8) hydrogen bonds : bond 0.19103 ( 592) hydrogen bonds : angle 7.94756 ( 1488) *********************** 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 : 0.590 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: 0.1255 time to fit residues: 82.1123 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 : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0970 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.177636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130054 restraints weight = 22897.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132580 restraints weight = 11737.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134776 restraints weight = 7895.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135279 restraints weight = 6201.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135580 restraints weight = 6025.773| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15634 Z= 0.141 Angle : 0.586 6.865 21220 Z= 0.309 Chirality : 0.045 0.151 2410 Planarity : 0.005 0.055 2704 Dihedral : 4.432 18.066 2100 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.68 % Allowed : 7.86 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.20), residues: 1930 helix: 1.89 (0.38), residues: 182 sheet: 1.33 (0.19), residues: 762 loop : 1.01 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 484 TYR 0.018 0.002 TYR F 141 PHE 0.017 0.001 PHE A 407 TRP 0.012 0.001 TRP D 141 HIS 0.005 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00326 (15630) covalent geometry : angle 0.58631 (21212) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.83204 ( 8) hydrogen bonds : bond 0.03958 ( 592) hydrogen bonds : angle 5.31243 ( 1488) *********************** 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 321 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 292 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9113 (t80) cc_final: 0.8753 (t80) REVERT: A 196 ASN cc_start: 0.8071 (m-40) cc_final: 0.7489 (p0) REVERT: A 247 MET cc_start: 0.8020 (tpt) cc_final: 0.7792 (tpt) REVERT: A 276 ASN cc_start: 0.8399 (t0) cc_final: 0.7539 (t0) REVERT: A 352 MET cc_start: 0.7533 (mtt) cc_final: 0.7266 (mtt) REVERT: A 407 PHE cc_start: 0.7679 (m-10) cc_final: 0.7391 (m-80) REVERT: A 474 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7808 (mt-10) REVERT: A 527 LYS cc_start: 0.7028 (pttt) cc_final: 0.6406 (mtpp) REVERT: A 554 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8479 (mtpt) REVERT: B 77 ASN cc_start: 0.8547 (t0) cc_final: 0.8162 (t0) REVERT: C 22 THR cc_start: 0.8582 (p) cc_final: 0.8336 (t) REVERT: C 140 PHE cc_start: 0.8255 (p90) cc_final: 0.7925 (p90) REVERT: C 167 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 193 PHE cc_start: 0.9112 (t80) cc_final: 0.8754 (t80) REVERT: D 196 ASN cc_start: 0.8068 (m-40) cc_final: 0.7491 (p0) REVERT: D 247 MET cc_start: 0.8028 (tpt) cc_final: 0.7802 (tpt) REVERT: D 276 ASN cc_start: 0.8399 (t0) cc_final: 0.7540 (t0) REVERT: D 352 MET cc_start: 0.7531 (mtt) cc_final: 0.7266 (mtt) REVERT: D 407 PHE cc_start: 0.7680 (m-10) cc_final: 0.7393 (m-80) REVERT: D 474 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7806 (mt-10) REVERT: D 527 LYS cc_start: 0.7031 (pttt) cc_final: 0.6408 (mtpp) REVERT: D 554 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8478 (mtpt) REVERT: E 77 ASN cc_start: 0.8548 (t0) cc_final: 0.8162 (t0) REVERT: F 22 THR cc_start: 0.8579 (p) cc_final: 0.8330 (t) REVERT: F 140 PHE cc_start: 0.8268 (p90) cc_final: 0.7907 (p90) REVERT: F 167 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7827 (tm-30) REVERT: F 177 SER cc_start: 0.8164 (t) cc_final: 0.7816 (p) REVERT: F 178 SER cc_start: 0.8238 (t) cc_final: 0.8026 (p) outliers start: 29 outliers final: 18 residues processed: 311 average time/residue: 0.1312 time to fit residues: 59.4323 Evaluate side-chains 244 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL 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 63 SER 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 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 63 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 6 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 101 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116177 restraints weight = 23583.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119931 restraints weight = 12895.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122432 restraints weight = 8934.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123931 restraints weight = 7105.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124758 restraints weight = 6187.306| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15634 Z= 0.234 Angle : 0.629 8.726 21220 Z= 0.329 Chirality : 0.047 0.155 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.604 20.069 2100 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.12 % Allowed : 8.79 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.20), residues: 1930 helix: 1.61 (0.38), residues: 186 sheet: 1.20 (0.19), residues: 802 loop : 0.60 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 102 TYR 0.020 0.002 TYR C 49 PHE 0.021 0.002 PHE D 583 TRP 0.016 0.002 TRP D 141 HIS 0.006 0.001 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00567 (15630) covalent geometry : angle 0.62914 (21212) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.79015 ( 8) hydrogen bonds : bond 0.04050 ( 592) hydrogen bonds : angle 5.21127 ( 1488) *********************** 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 284 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8261 (m-40) cc_final: 0.7686 (p0) REVERT: A 278 GLU cc_start: 0.7912 (pm20) cc_final: 0.7677 (pm20) REVERT: A 464 SER cc_start: 0.9247 (p) cc_final: 0.8912 (t) REVERT: A 527 LYS cc_start: 0.7334 (pttt) cc_final: 0.6748 (mtpp) REVERT: A 543 GLU cc_start: 0.7898 (tt0) cc_final: 0.7681 (tt0) REVERT: B 77 ASN cc_start: 0.8578 (t0) cc_final: 0.7874 (t0) REVERT: C 22 THR cc_start: 0.8586 (p) cc_final: 0.8362 (t) REVERT: D 196 ASN cc_start: 0.8261 (m-40) cc_final: 0.7686 (p0) REVERT: D 278 GLU cc_start: 0.7912 (pm20) cc_final: 0.7675 (pm20) REVERT: D 464 SER cc_start: 0.9258 (p) cc_final: 0.8920 (t) REVERT: D 527 LYS cc_start: 0.7336 (pttt) cc_final: 0.6753 (mtpp) REVERT: D 543 GLU cc_start: 0.7885 (tt0) cc_final: 0.7674 (tt0) REVERT: E 77 ASN cc_start: 0.8579 (t0) cc_final: 0.7878 (t0) REVERT: F 22 THR cc_start: 0.8586 (p) cc_final: 0.8366 (t) REVERT: F 137 LEU cc_start: 0.8673 (mm) cc_final: 0.8216 (mp) outliers start: 54 outliers final: 33 residues processed: 262 average time/residue: 0.1339 time to fit residues: 50.8901 Evaluate side-chains 233 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 208 MET 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 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 182 LEU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 274 THR 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 75 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 194 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN D 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.171204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121000 restraints weight = 23304.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124907 restraints weight = 12552.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127445 restraints weight = 8587.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129102 restraints weight = 6763.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130114 restraints weight = 5820.385| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15634 Z= 0.130 Angle : 0.548 7.583 21220 Z= 0.281 Chirality : 0.044 0.187 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.242 17.358 2100 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.20 % Allowed : 11.04 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1930 helix: 1.30 (0.38), residues: 204 sheet: 1.38 (0.19), residues: 788 loop : 0.57 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.013 0.001 TYR C 49 PHE 0.010 0.001 PHE A 583 TRP 0.009 0.001 TRP D 141 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00308 (15630) covalent geometry : angle 0.54772 (21212) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.64703 ( 8) hydrogen bonds : bond 0.03383 ( 592) hydrogen bonds : angle 4.86653 ( 1488) *********************** 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 271 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8461 (pt0) cc_final: 0.8234 (pt0) REVERT: A 193 PHE cc_start: 0.9126 (t80) cc_final: 0.8918 (t80) REVERT: A 196 ASN cc_start: 0.8243 (m-40) cc_final: 0.7699 (p0) REVERT: A 278 GLU cc_start: 0.7889 (pm20) cc_final: 0.7617 (pm20) REVERT: A 461 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8126 (ttmt) REVERT: A 464 SER cc_start: 0.9240 (p) cc_final: 0.8900 (t) REVERT: A 527 LYS cc_start: 0.7404 (pttt) cc_final: 0.6779 (mtpp) REVERT: B 77 ASN cc_start: 0.8576 (t0) cc_final: 0.7941 (t0) REVERT: C 22 THR cc_start: 0.8593 (p) cc_final: 0.8341 (t) REVERT: C 42 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8473 (mttp) REVERT: D 146 GLN cc_start: 0.8467 (pt0) cc_final: 0.8236 (pt0) REVERT: D 193 PHE cc_start: 0.9128 (t80) cc_final: 0.8920 (t80) REVERT: D 196 ASN cc_start: 0.8236 (m-40) cc_final: 0.7694 (p0) REVERT: D 278 GLU cc_start: 0.7887 (pm20) cc_final: 0.7613 (pm20) REVERT: D 461 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8129 (ttmt) REVERT: D 464 SER cc_start: 0.9240 (p) cc_final: 0.8902 (t) REVERT: D 527 LYS cc_start: 0.7397 (pttt) cc_final: 0.6778 (mtpp) REVERT: E 77 ASN cc_start: 0.8586 (t0) cc_final: 0.7953 (t0) REVERT: F 22 THR cc_start: 0.8597 (p) cc_final: 0.8348 (t) REVERT: F 42 LYS cc_start: 0.8840 (mmtp) cc_final: 0.8473 (mttp) outliers start: 38 outliers final: 17 residues processed: 257 average time/residue: 0.1324 time to fit residues: 48.5429 Evaluate side-chains 219 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain B residue 37 VAL 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 121 ILE Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 37 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.0030 chunk 103 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.168354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120159 restraints weight = 23325.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123282 restraints weight = 11840.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124135 restraints weight = 7977.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124690 restraints weight = 7236.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124733 restraints weight = 6567.531| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4488 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= 0.182 Angle : 0.578 8.730 21220 Z= 0.296 Chirality : 0.045 0.189 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.350 17.729 2100 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.95 % Allowed : 10.75 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 1930 helix: 1.34 (0.38), residues: 202 sheet: 1.32 (0.18), residues: 790 loop : 0.42 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 218 TYR 0.017 0.002 TYR F 49 PHE 0.016 0.001 PHE D 583 TRP 0.010 0.002 TRP D 141 HIS 0.005 0.001 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00443 (15630) covalent geometry : angle 0.57795 (21212) SS BOND : bond 0.00041 ( 4) SS BOND : angle 0.63166 ( 8) hydrogen bonds : bond 0.03524 ( 592) hydrogen bonds : angle 4.90274 ( 1488) *********************** 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 269 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8565 (pt0) cc_final: 0.8341 (pt0) REVERT: A 196 ASN cc_start: 0.8316 (m-40) cc_final: 0.7746 (p0) REVERT: A 278 GLU cc_start: 0.7973 (pm20) cc_final: 0.7690 (pm20) REVERT: A 464 SER cc_start: 0.9233 (p) cc_final: 0.8901 (t) REVERT: A 527 LYS cc_start: 0.7386 (pttt) cc_final: 0.6774 (mtpp) REVERT: A 576 PHE cc_start: 0.7382 (m-80) cc_final: 0.7058 (t80) REVERT: B 77 ASN cc_start: 0.8607 (t0) cc_final: 0.8036 (t0) REVERT: B 89 GLU cc_start: 0.8731 (pm20) cc_final: 0.8508 (pm20) REVERT: C 22 THR cc_start: 0.8635 (p) cc_final: 0.8409 (t) REVERT: C 42 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8524 (mttp) REVERT: D 146 GLN cc_start: 0.8566 (pt0) cc_final: 0.8349 (pt0) REVERT: D 196 ASN cc_start: 0.8317 (m-40) cc_final: 0.7745 (p0) REVERT: D 278 GLU cc_start: 0.7973 (pm20) cc_final: 0.7688 (pm20) REVERT: D 464 SER cc_start: 0.9234 (p) cc_final: 0.8898 (t) REVERT: D 527 LYS cc_start: 0.7382 (pttt) cc_final: 0.6771 (mtpp) REVERT: D 576 PHE cc_start: 0.7370 (m-80) cc_final: 0.7049 (t80) REVERT: E 77 ASN cc_start: 0.8610 (t0) cc_final: 0.8046 (t0) REVERT: F 22 THR cc_start: 0.8637 (p) cc_final: 0.8413 (t) REVERT: F 42 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8525 (mttp) outliers start: 51 outliers final: 33 residues processed: 247 average time/residue: 0.1267 time to fit residues: 45.3274 Evaluate side-chains 233 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR 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 328 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 160 VAL 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 87 THR 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 328 MET Chi-restraints excluded: chain D residue 596 LEU 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 96 CYS Chi-restraints excluded: chain E residue 160 VAL 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 69 optimal weight: 30.0000 chunk 168 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 151 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.167991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118175 restraints weight = 23267.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121903 restraints weight = 12517.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124390 restraints weight = 8583.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125940 restraints weight = 6797.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126873 restraints weight = 5878.414| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15634 Z= 0.165 Angle : 0.569 9.236 21220 Z= 0.288 Chirality : 0.044 0.189 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.266 18.051 2100 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.37 % Allowed : 11.27 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.19), residues: 1930 helix: 1.49 (0.38), residues: 202 sheet: 1.30 (0.19), residues: 778 loop : 0.31 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.016 0.001 TYR C 49 PHE 0.017 0.002 PHE A 40 TRP 0.015 0.002 TRP C 35 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00403 (15630) covalent geometry : angle 0.56867 (21212) SS BOND : bond 0.00049 ( 4) SS BOND : angle 0.60215 ( 8) hydrogen bonds : bond 0.03389 ( 592) hydrogen bonds : angle 4.84152 ( 1488) *********************** 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: 41 poor density : 221 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9001 (t80) cc_final: 0.8570 (t80) REVERT: A 196 ASN cc_start: 0.8256 (m-40) cc_final: 0.7711 (p0) REVERT: A 278 GLU cc_start: 0.7980 (pm20) cc_final: 0.7685 (pm20) REVERT: A 464 SER cc_start: 0.9255 (p) cc_final: 0.8925 (t) REVERT: A 527 LYS cc_start: 0.7445 (pttt) cc_final: 0.6835 (mtpp) REVERT: A 576 PHE cc_start: 0.7387 (m-80) cc_final: 0.7052 (t80) REVERT: B 77 ASN cc_start: 0.8569 (t0) cc_final: 0.7937 (t0) REVERT: B 89 GLU cc_start: 0.8848 (pm20) cc_final: 0.8622 (pm20) REVERT: C 42 LYS cc_start: 0.8846 (mmtp) cc_final: 0.8533 (mttp) REVERT: D 193 PHE cc_start: 0.8999 (t80) cc_final: 0.8569 (t80) REVERT: D 196 ASN cc_start: 0.8254 (m-40) cc_final: 0.7712 (p0) REVERT: D 278 GLU cc_start: 0.7976 (pm20) cc_final: 0.7681 (pm20) REVERT: D 464 SER cc_start: 0.9252 (p) cc_final: 0.8915 (t) REVERT: D 527 LYS cc_start: 0.7440 (pttt) cc_final: 0.6833 (mtpp) REVERT: D 576 PHE cc_start: 0.7376 (m-80) cc_final: 0.7042 (t80) REVERT: E 77 ASN cc_start: 0.8566 (t0) cc_final: 0.7933 (t0) REVERT: F 42 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8537 (mttp) outliers start: 41 outliers final: 38 residues processed: 249 average time/residue: 0.1386 time to fit residues: 50.0858 Evaluate side-chains 242 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR 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 328 MET Chi-restraints excluded: chain A residue 596 LEU 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 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 87 THR 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 328 MET Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 596 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 115 optimal weight: 0.0070 chunk 157 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.170999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121403 restraints weight = 22893.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125230 restraints weight = 12284.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127743 restraints weight = 8409.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129352 restraints weight = 6626.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130363 restraints weight = 5712.545| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15634 Z= 0.109 Angle : 0.543 8.876 21220 Z= 0.272 Chirality : 0.043 0.181 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.030 17.186 2100 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.31 % Allowed : 12.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.20), residues: 1930 helix: 1.72 (0.38), residues: 202 sheet: 1.36 (0.19), residues: 778 loop : 0.41 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.013 0.001 TYR C 49 PHE 0.010 0.001 PHE D 582 TRP 0.008 0.001 TRP B 162 HIS 0.003 0.001 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00259 (15630) covalent geometry : angle 0.54304 (21212) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.57405 ( 8) hydrogen bonds : bond 0.03080 ( 592) hydrogen bonds : angle 4.63807 ( 1488) *********************** 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 259 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8954 (t80) cc_final: 0.8391 (t80) REVERT: A 196 ASN cc_start: 0.8260 (m-40) cc_final: 0.7828 (p0) REVERT: A 278 GLU cc_start: 0.7928 (pm20) cc_final: 0.7643 (pm20) REVERT: A 464 SER cc_start: 0.9236 (p) cc_final: 0.8913 (t) REVERT: A 527 LYS cc_start: 0.7437 (pttt) cc_final: 0.6860 (mtpp) REVERT: A 576 PHE cc_start: 0.7374 (m-80) cc_final: 0.7028 (t80) REVERT: B 77 ASN cc_start: 0.8552 (t0) cc_final: 0.8026 (t0) REVERT: B 89 GLU cc_start: 0.8888 (pm20) cc_final: 0.8639 (pm20) REVERT: C 42 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8554 (mttp) REVERT: D 193 PHE cc_start: 0.8957 (t80) cc_final: 0.8393 (t80) REVERT: D 196 ASN cc_start: 0.8263 (m-40) cc_final: 0.7832 (p0) REVERT: D 278 GLU cc_start: 0.7915 (pm20) cc_final: 0.7634 (pm20) REVERT: D 464 SER cc_start: 0.9232 (p) cc_final: 0.8907 (t) REVERT: D 527 LYS cc_start: 0.7429 (pttt) cc_final: 0.6856 (mtpp) REVERT: D 576 PHE cc_start: 0.7367 (m-80) cc_final: 0.7022 (t80) REVERT: E 77 ASN cc_start: 0.8549 (t0) cc_final: 0.8015 (t0) REVERT: F 42 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8556 (mttp) outliers start: 40 outliers final: 26 residues processed: 242 average time/residue: 0.1491 time to fit residues: 51.2102 Evaluate side-chains 224 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 74 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 328 MET Chi-restraints excluded: chain D residue 389 PHE 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 96 CYS Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.169758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119919 restraints weight = 23457.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123741 restraints weight = 12488.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126253 restraints weight = 8518.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127821 restraints weight = 6720.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128860 restraints weight = 5799.351| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4969 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= 0.134 Angle : 0.553 9.296 21220 Z= 0.277 Chirality : 0.044 0.185 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.078 16.957 2100 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.91 % Allowed : 12.72 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.20), residues: 1930 helix: 1.80 (0.39), residues: 204 sheet: 1.33 (0.19), residues: 778 loop : 0.32 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 218 TYR 0.014 0.001 TYR C 49 PHE 0.018 0.001 PHE D 40 TRP 0.009 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00325 (15630) covalent geometry : angle 0.55289 (21212) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.55974 ( 8) hydrogen bonds : bond 0.03113 ( 592) hydrogen bonds : angle 4.64108 ( 1488) *********************** 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 234 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8983 (t80) cc_final: 0.8443 (t80) REVERT: A 196 ASN cc_start: 0.8279 (m-40) cc_final: 0.7864 (p0) REVERT: A 278 GLU cc_start: 0.7932 (pm20) cc_final: 0.7625 (pm20) REVERT: A 464 SER cc_start: 0.9246 (p) cc_final: 0.8950 (t) REVERT: A 527 LYS cc_start: 0.7440 (pttt) cc_final: 0.6888 (mtpp) REVERT: A 576 PHE cc_start: 0.7371 (m-80) cc_final: 0.7022 (t80) REVERT: B 77 ASN cc_start: 0.8546 (t0) cc_final: 0.8092 (t0) REVERT: B 89 GLU cc_start: 0.8932 (pm20) cc_final: 0.8703 (pm20) REVERT: C 42 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8544 (mttp) REVERT: D 193 PHE cc_start: 0.8983 (t80) cc_final: 0.8446 (t80) REVERT: D 196 ASN cc_start: 0.8276 (m-40) cc_final: 0.7867 (p0) REVERT: D 278 GLU cc_start: 0.7927 (pm20) cc_final: 0.7618 (pm20) REVERT: D 464 SER cc_start: 0.9244 (p) cc_final: 0.8945 (t) REVERT: D 527 LYS cc_start: 0.7433 (pttt) cc_final: 0.6885 (mtpp) REVERT: D 576 PHE cc_start: 0.7367 (m-80) cc_final: 0.7019 (t80) REVERT: E 77 ASN cc_start: 0.8560 (t0) cc_final: 0.8104 (t0) REVERT: F 42 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8544 (mttp) outliers start: 33 outliers final: 31 residues processed: 219 average time/residue: 0.1305 time to fit residues: 42.1003 Evaluate side-chains 223 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 148 optimal weight: 0.3980 chunk 192 optimal weight: 0.0370 chunk 179 optimal weight: 0.2980 chunk 165 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.173897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124789 restraints weight = 23109.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128715 restraints weight = 12170.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131286 restraints weight = 8236.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132879 restraints weight = 6462.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133917 restraints weight = 5567.800| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15634 Z= 0.094 Angle : 0.532 8.680 21220 Z= 0.263 Chirality : 0.043 0.173 2410 Planarity : 0.004 0.047 2704 Dihedral : 3.840 15.782 2100 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.50 % Allowed : 13.06 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.20), residues: 1930 helix: 1.92 (0.38), residues: 204 sheet: 1.41 (0.19), residues: 782 loop : 0.46 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 218 TYR 0.010 0.001 TYR C 49 PHE 0.017 0.001 PHE A 40 TRP 0.008 0.001 TRP A 659 HIS 0.002 0.000 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00216 (15630) covalent geometry : angle 0.53182 (21212) SS BOND : bond 0.00061 ( 4) SS BOND : angle 0.49296 ( 8) hydrogen bonds : bond 0.02794 ( 592) hydrogen bonds : angle 4.42910 ( 1488) *********************** 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 237 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8895 (t80) cc_final: 0.8302 (t80) REVERT: A 196 ASN cc_start: 0.8197 (m-40) cc_final: 0.7823 (p0) REVERT: A 278 GLU cc_start: 0.7877 (pm20) cc_final: 0.7577 (pm20) REVERT: A 464 SER cc_start: 0.9232 (p) cc_final: 0.8953 (t) REVERT: A 527 LYS cc_start: 0.7409 (pttt) cc_final: 0.6933 (mtpp) REVERT: A 576 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 77 ASN cc_start: 0.8478 (t0) cc_final: 0.8025 (t0) REVERT: B 89 GLU cc_start: 0.8928 (pm20) cc_final: 0.8723 (pm20) REVERT: D 193 PHE cc_start: 0.8899 (t80) cc_final: 0.8304 (t80) REVERT: D 196 ASN cc_start: 0.8197 (m-40) cc_final: 0.7828 (p0) REVERT: D 278 GLU cc_start: 0.7864 (pm20) cc_final: 0.7564 (pm20) REVERT: D 464 SER cc_start: 0.9231 (p) cc_final: 0.8947 (t) REVERT: D 527 LYS cc_start: 0.7406 (pttt) cc_final: 0.6932 (mtpp) REVERT: D 576 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.7001 (t80) REVERT: E 77 ASN cc_start: 0.8481 (t0) cc_final: 0.8019 (t0) outliers start: 26 outliers final: 16 residues processed: 228 average time/residue: 0.1288 time to fit residues: 43.7724 Evaluate side-chains 210 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 389 PHE Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 74 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 389 PHE Chi-restraints excluded: chain D residue 576 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.170728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120939 restraints weight = 23360.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124798 restraints weight = 12429.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127290 restraints weight = 8453.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128903 restraints weight = 6653.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129779 restraints weight = 5751.287| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15634 Z= 0.135 Angle : 0.564 9.542 21220 Z= 0.283 Chirality : 0.044 0.185 2410 Planarity : 0.005 0.047 2704 Dihedral : 3.969 16.438 2100 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.21 % Allowed : 13.82 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.20), residues: 1930 helix: 1.97 (0.39), residues: 204 sheet: 1.41 (0.19), residues: 778 loop : 0.40 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 218 TYR 0.014 0.001 TYR F 49 PHE 0.018 0.001 PHE A 40 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00327 (15630) covalent geometry : angle 0.56399 (21212) SS BOND : bond 0.00033 ( 4) SS BOND : angle 0.46388 ( 8) hydrogen bonds : bond 0.03007 ( 592) hydrogen bonds : angle 4.50778 ( 1488) ********************** 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 213 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8906 (t80) cc_final: 0.8323 (t80) REVERT: A 196 ASN cc_start: 0.8283 (m-40) cc_final: 0.7884 (p0) REVERT: A 278 GLU cc_start: 0.7933 (pm20) cc_final: 0.7616 (pm20) REVERT: A 464 SER cc_start: 0.9226 (p) cc_final: 0.8978 (t) REVERT: A 527 LYS cc_start: 0.7446 (pttt) cc_final: 0.6941 (mtpp) REVERT: A 576 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7014 (t80) REVERT: B 77 ASN cc_start: 0.8519 (t0) cc_final: 0.8075 (t0) REVERT: D 188 LYS cc_start: 0.7790 (tttt) cc_final: 0.7487 (tttt) REVERT: D 193 PHE cc_start: 0.8908 (t80) cc_final: 0.8327 (t80) REVERT: D 196 ASN cc_start: 0.8282 (m-40) cc_final: 0.7885 (p0) REVERT: D 278 GLU cc_start: 0.7928 (pm20) cc_final: 0.7609 (pm20) REVERT: D 464 SER cc_start: 0.9226 (p) cc_final: 0.8973 (t) REVERT: D 527 LYS cc_start: 0.7445 (pttt) cc_final: 0.6940 (mtpp) REVERT: D 576 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7007 (t80) REVERT: E 77 ASN cc_start: 0.8515 (t0) cc_final: 0.8058 (t0) outliers start: 21 outliers final: 19 residues processed: 203 average time/residue: 0.1233 time to fit residues: 36.9213 Evaluate side-chains 209 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 389 PHE Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 VAL 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 389 PHE Chi-restraints excluded: chain D residue 576 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 162 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 190 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.172805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126376 restraints weight = 23044.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129977 restraints weight = 11546.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130805 restraints weight = 7570.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131336 restraints weight = 6642.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131335 restraints weight = 6088.062| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5212 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= 0.106 Angle : 0.554 9.058 21220 Z= 0.276 Chirality : 0.043 0.177 2410 Planarity : 0.005 0.047 2704 Dihedral : 3.876 15.855 2100 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.10 % Allowed : 14.05 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.20), residues: 1930 helix: 1.94 (0.38), residues: 204 sheet: 1.47 (0.19), residues: 778 loop : 0.44 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 87 TYR 0.012 0.001 TYR F 49 PHE 0.018 0.001 PHE D 40 TRP 0.007 0.001 TRP B 162 HIS 0.002 0.001 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00251 (15630) covalent geometry : angle 0.55395 (21212) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.46434 ( 8) hydrogen bonds : bond 0.02838 ( 592) hydrogen bonds : angle 4.40596 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.55 seconds wall clock time: 53 minutes 4.66 seconds (3184.66 seconds total)