Starting phenix.real_space_refine on Mon Nov 18 04:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/11_2024/8smk_40589.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/11_2024/8smk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/11_2024/8smk_40589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/11_2024/8smk_40589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/11_2024/8smk_40589.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/11_2024/8smk_40589.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.387 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 82 5.16 5 C 9712 2.51 5 N 2556 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4348 Classifications: {'peptide': 555} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 520} Chain breaks: 10 Chain: "B" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1653 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain: "C" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1644 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: D, F, E Time building chain proxies: 12.43, per 1000 atoms: 0.81 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=2, 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 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: 4.22 Conformation dependent library (CDL) restraints added in 2.1 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 44 sheets defined 15.3% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 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: 9.74 Time building geometry restraints manager: 4.78 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: 9043 16.99 - 33.98: 220 33.98 - 50.97: 49 50.97 - 67.95: 50 67.95 - 84.94: 18 Dihedral angle restraints: 9380 sinusoidal: 3656 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 9377 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: 2.04 - 2.61: 60 2.61 - 3.19: 12408 3.19 - 3.76: 22295 3.76 - 4.33: 32783 4.33 - 4.90: 53379 Nonbonded interactions: 120925 Sorted by model distance: nonbonded pdb=" SG CYS F 135 " pdb=" SG CYS F 195 " model vdw 2.043 3.760 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 ... (remaining 120920 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: 0.00 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.140 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- 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 0.069 15630 Z= 0.748 Angle : 1.376 8.897 21212 Z= 0.958 Chirality : 0.064 0.322 2410 Planarity : 0.008 0.083 2704 Dihedral : 11.016 84.943 5678 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1930 helix: 0.55 (0.36), residues: 180 sheet: 1.12 (0.19), residues: 690 loop : 0.86 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP A 466 HIS 0.002 0.000 HIS C 199 PHE 0.039 0.003 PHE D 487 TYR 0.107 0.003 TYR E 105 ARG 0.009 0.001 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.718 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: 0.3129 time to fit residues: 201.8222 Evaluate side-chains 270 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.0050 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 471 HIS D 245 HIS D 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15630 Z= 0.192 Angle : 0.576 7.072 21212 Z= 0.304 Chirality : 0.045 0.150 2410 Planarity : 0.005 0.055 2704 Dihedral : 4.416 17.678 2100 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.73 % Allowed : 7.69 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1930 helix: 1.88 (0.38), residues: 182 sheet: 1.29 (0.19), residues: 772 loop : 1.07 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 141 HIS 0.005 0.001 HIS D 245 PHE 0.017 0.001 PHE A 407 TYR 0.017 0.002 TYR F 141 ARG 0.003 0.001 ARG A 484 *********************** 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 326 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8304 (m) REVERT: A 175 GLU cc_start: 0.8454 (mp0) cc_final: 0.8146 (pm20) REVERT: A 188 LYS cc_start: 0.7669 (tttt) cc_final: 0.7134 (tttt) REVERT: A 193 PHE cc_start: 0.9162 (t80) cc_final: 0.8712 (t80) REVERT: A 196 ASN cc_start: 0.8059 (m-40) cc_final: 0.7316 (p0) REVERT: A 244 LYS cc_start: 0.8494 (tptt) cc_final: 0.7496 (tptt) REVERT: A 247 MET cc_start: 0.8032 (tpt) cc_final: 0.7827 (tpt) REVERT: A 276 ASN cc_start: 0.8360 (t0) cc_final: 0.7893 (t0) REVERT: A 352 MET cc_start: 0.7512 (mtt) cc_final: 0.7249 (mtt) REVERT: A 407 PHE cc_start: 0.7441 (m-10) cc_final: 0.7128 (m-80) REVERT: A 474 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7908 (mt-10) REVERT: A 527 LYS cc_start: 0.6912 (pttt) cc_final: 0.6314 (mtpp) REVERT: A 554 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8327 (mtpt) REVERT: B 77 ASN cc_start: 0.8666 (t0) cc_final: 0.8273 (t0) REVERT: C 22 THR cc_start: 0.8541 (p) cc_final: 0.8281 (t) REVERT: C 140 PHE cc_start: 0.8221 (p90) cc_final: 0.7775 (p90) REVERT: C 167 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7820 (tm-30) REVERT: D 45 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 175 GLU cc_start: 0.8458 (mp0) cc_final: 0.8146 (pm20) REVERT: D 188 LYS cc_start: 0.7662 (tttt) cc_final: 0.7122 (tttt) REVERT: D 193 PHE cc_start: 0.9163 (t80) cc_final: 0.8710 (t80) REVERT: D 196 ASN cc_start: 0.8053 (m-40) cc_final: 0.7315 (p0) REVERT: D 244 LYS cc_start: 0.8494 (tptt) cc_final: 0.7496 (tptt) REVERT: D 276 ASN cc_start: 0.8362 (t0) cc_final: 0.7891 (t0) REVERT: D 352 MET cc_start: 0.7513 (mtt) cc_final: 0.7254 (mtt) REVERT: D 407 PHE cc_start: 0.7431 (m-10) cc_final: 0.7120 (m-80) REVERT: D 474 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7906 (mt-10) REVERT: D 527 LYS cc_start: 0.6911 (pttt) cc_final: 0.6314 (mtpp) REVERT: D 554 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8320 (mtpt) REVERT: E 77 ASN cc_start: 0.8667 (t0) cc_final: 0.8272 (t0) REVERT: F 22 THR cc_start: 0.8559 (p) cc_final: 0.8295 (t) REVERT: F 140 PHE cc_start: 0.8224 (p90) cc_final: 0.7769 (p90) REVERT: F 167 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7826 (tm-30) REVERT: F 177 SER cc_start: 0.8137 (t) cc_final: 0.7799 (p) outliers start: 30 outliers final: 16 residues processed: 314 average time/residue: 0.3038 time to fit residues: 137.1522 Evaluate side-chains 246 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15630 Z= 0.366 Angle : 0.634 9.158 21212 Z= 0.331 Chirality : 0.047 0.163 2410 Planarity : 0.005 0.048 2704 Dihedral : 4.633 19.995 2100 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.18 % Allowed : 8.96 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1930 helix: 1.57 (0.39), residues: 186 sheet: 1.20 (0.18), residues: 802 loop : 0.58 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 141 HIS 0.006 0.001 HIS D 236 PHE 0.021 0.002 PHE D 583 TYR 0.023 0.002 TYR E 153 ARG 0.004 0.001 ARG B 102 *********************** 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 296 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.8488 (mp0) cc_final: 0.8191 (pm20) REVERT: A 193 PHE cc_start: 0.9310 (t80) cc_final: 0.8841 (t80) REVERT: A 196 ASN cc_start: 0.8290 (m-40) cc_final: 0.7519 (p0) REVERT: A 278 GLU cc_start: 0.8022 (pm20) cc_final: 0.7772 (pm20) REVERT: A 464 SER cc_start: 0.9245 (p) cc_final: 0.8857 (t) REVERT: A 527 LYS cc_start: 0.7129 (pttt) cc_final: 0.6542 (mtpp) REVERT: A 543 GLU cc_start: 0.7940 (tt0) cc_final: 0.7651 (tt0) REVERT: A 626 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7699 (mp10) REVERT: B 7 SER cc_start: 0.8758 (t) cc_final: 0.8505 (p) REVERT: B 77 ASN cc_start: 0.8681 (t0) cc_final: 0.8320 (t0) REVERT: C 22 THR cc_start: 0.8546 (p) cc_final: 0.8294 (t) REVERT: D 175 GLU cc_start: 0.8486 (mp0) cc_final: 0.8194 (pm20) REVERT: D 193 PHE cc_start: 0.9312 (t80) cc_final: 0.8843 (t80) REVERT: D 196 ASN cc_start: 0.8288 (m-40) cc_final: 0.7522 (p0) REVERT: D 278 GLU cc_start: 0.8012 (pm20) cc_final: 0.7763 (pm20) REVERT: D 464 SER cc_start: 0.9241 (p) cc_final: 0.8838 (t) REVERT: D 527 LYS cc_start: 0.7125 (pttt) cc_final: 0.6537 (mtpp) REVERT: D 543 GLU cc_start: 0.7939 (tt0) cc_final: 0.7655 (tt0) REVERT: E 7 SER cc_start: 0.8763 (t) cc_final: 0.8521 (p) REVERT: E 77 ASN cc_start: 0.8679 (t0) cc_final: 0.8318 (t0) REVERT: F 22 THR cc_start: 0.8563 (p) cc_final: 0.8309 (t) outliers start: 55 outliers final: 38 residues processed: 273 average time/residue: 0.3103 time to fit residues: 121.9033 Evaluate side-chains 252 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 596 LEU Chi-restraints excluded: chain A residue 606 ILE 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 183 MET 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 596 LEU Chi-restraints excluded: chain D residue 606 ILE 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 176 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15630 Z= 0.279 Angle : 0.567 8.251 21212 Z= 0.294 Chirality : 0.045 0.198 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.391 17.888 2100 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.12 % Allowed : 10.00 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1930 helix: 1.21 (0.37), residues: 202 sheet: 1.29 (0.19), residues: 790 loop : 0.47 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 PHE 0.013 0.001 PHE D 583 TYR 0.015 0.002 TYR F 49 ARG 0.003 0.001 ARG F 24 *********************** 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 293 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7718 (mp0) REVERT: A 175 GLU cc_start: 0.8489 (mp0) cc_final: 0.8197 (pm20) REVERT: A 193 PHE cc_start: 0.9233 (t80) cc_final: 0.8751 (t80) REVERT: A 196 ASN cc_start: 0.8318 (m-40) cc_final: 0.7580 (p0) REVERT: A 278 GLU cc_start: 0.7983 (pm20) cc_final: 0.7684 (pm20) REVERT: A 464 SER cc_start: 0.9259 (p) cc_final: 0.8885 (t) REVERT: A 527 LYS cc_start: 0.7242 (pttt) cc_final: 0.6638 (mtpp) REVERT: B 7 SER cc_start: 0.8747 (t) cc_final: 0.8470 (p) REVERT: B 77 ASN cc_start: 0.8685 (t0) cc_final: 0.8043 (t0) REVERT: B 89 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: C 22 THR cc_start: 0.8598 (p) cc_final: 0.8334 (t) REVERT: C 61 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7950 (mtm110) REVERT: D 146 GLN cc_start: 0.8625 (pt0) cc_final: 0.8353 (pt0) REVERT: D 170 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7731 (mp0) REVERT: D 175 GLU cc_start: 0.8491 (mp0) cc_final: 0.8202 (pm20) REVERT: D 193 PHE cc_start: 0.9234 (t80) cc_final: 0.8749 (t80) REVERT: D 196 ASN cc_start: 0.8318 (m-40) cc_final: 0.7586 (p0) REVERT: D 278 GLU cc_start: 0.7972 (pm20) cc_final: 0.7672 (pm20) REVERT: D 464 SER cc_start: 0.9258 (p) cc_final: 0.8862 (t) REVERT: D 527 LYS cc_start: 0.7243 (pttt) cc_final: 0.6638 (mtpp) REVERT: E 7 SER cc_start: 0.8752 (t) cc_final: 0.8484 (p) REVERT: E 77 ASN cc_start: 0.8681 (t0) cc_final: 0.8040 (t0) REVERT: F 22 THR cc_start: 0.8615 (p) cc_final: 0.8350 (t) REVERT: F 61 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7953 (mtm110) outliers start: 54 outliers final: 33 residues processed: 269 average time/residue: 0.3149 time to fit residues: 121.0942 Evaluate side-chains 245 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 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 468 SER Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 89 GLU 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 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 468 SER Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.0170 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15630 Z= 0.186 Angle : 0.542 7.688 21212 Z= 0.275 Chirality : 0.044 0.182 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.141 16.864 2100 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.31 % Allowed : 11.50 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1930 helix: 1.33 (0.37), residues: 202 sheet: 1.39 (0.18), residues: 790 loop : 0.49 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 659 HIS 0.003 0.001 HIS D 236 PHE 0.015 0.001 PHE D 40 TYR 0.013 0.001 TYR C 49 ARG 0.007 0.001 ARG A 218 *********************** 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 277 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8612 (pt0) cc_final: 0.8374 (pt0) REVERT: A 193 PHE cc_start: 0.9198 (t80) cc_final: 0.8756 (t80) REVERT: A 196 ASN cc_start: 0.8312 (m-40) cc_final: 0.7657 (p0) REVERT: A 278 GLU cc_start: 0.7935 (pm20) cc_final: 0.7531 (pm20) REVERT: A 464 SER cc_start: 0.9240 (p) cc_final: 0.8852 (t) REVERT: A 527 LYS cc_start: 0.7266 (pttt) cc_final: 0.6662 (mtpp) REVERT: A 576 PHE cc_start: 0.7560 (m-80) cc_final: 0.7195 (t80) REVERT: B 7 SER cc_start: 0.8765 (t) cc_final: 0.8486 (p) REVERT: B 77 ASN cc_start: 0.8642 (t0) cc_final: 0.8064 (t0) REVERT: B 89 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: C 22 THR cc_start: 0.8606 (p) cc_final: 0.8365 (t) REVERT: C 42 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8456 (mttp) REVERT: D 146 GLN cc_start: 0.8604 (pt0) cc_final: 0.8370 (pt0) REVERT: D 193 PHE cc_start: 0.9199 (t80) cc_final: 0.8757 (t80) REVERT: D 196 ASN cc_start: 0.8314 (m-40) cc_final: 0.7659 (p0) REVERT: D 278 GLU cc_start: 0.7923 (pm20) cc_final: 0.7516 (pm20) REVERT: D 464 SER cc_start: 0.9235 (p) cc_final: 0.8837 (t) REVERT: D 527 LYS cc_start: 0.7261 (pttt) cc_final: 0.6659 (mtpp) REVERT: D 576 PHE cc_start: 0.7563 (m-80) cc_final: 0.7202 (t80) REVERT: E 7 SER cc_start: 0.8765 (t) cc_final: 0.8500 (p) REVERT: E 77 ASN cc_start: 0.8637 (t0) cc_final: 0.8068 (t0) REVERT: F 22 THR cc_start: 0.8618 (p) cc_final: 0.8376 (t) REVERT: F 42 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8457 (mttp) outliers start: 40 outliers final: 26 residues processed: 261 average time/residue: 0.3111 time to fit residues: 116.6293 Evaluate side-chains 241 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 184 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.7980 chunk 170 optimal weight: 0.0070 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15630 Z= 0.168 Angle : 0.541 7.879 21212 Z= 0.270 Chirality : 0.043 0.178 2410 Planarity : 0.005 0.047 2704 Dihedral : 3.991 16.956 2100 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 12.02 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1930 helix: 1.57 (0.37), residues: 202 sheet: 1.47 (0.18), residues: 790 loop : 0.48 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 139 HIS 0.003 0.001 HIS D 236 PHE 0.014 0.001 PHE D 582 TYR 0.012 0.001 TYR C 49 ARG 0.004 0.000 ARG D 218 *********************** 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 252 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8592 (pt0) cc_final: 0.8332 (pt0) REVERT: A 193 PHE cc_start: 0.9178 (t80) cc_final: 0.8759 (t80) REVERT: A 196 ASN cc_start: 0.8329 (m-40) cc_final: 0.7666 (p0) REVERT: A 278 GLU cc_start: 0.7986 (pm20) cc_final: 0.7606 (pm20) REVERT: A 298 MET cc_start: 0.8810 (ttt) cc_final: 0.8577 (ttt) REVERT: A 464 SER cc_start: 0.9252 (p) cc_final: 0.8862 (t) REVERT: A 527 LYS cc_start: 0.7275 (pttt) cc_final: 0.6704 (mtpp) REVERT: A 576 PHE cc_start: 0.7563 (m-80) cc_final: 0.7180 (t80) REVERT: B 7 SER cc_start: 0.8745 (t) cc_final: 0.8500 (p) REVERT: B 77 ASN cc_start: 0.8606 (t0) cc_final: 0.8047 (t0) REVERT: B 90 ASP cc_start: 0.8463 (m-30) cc_final: 0.8241 (m-30) REVERT: C 42 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8454 (mttp) REVERT: D 146 GLN cc_start: 0.8583 (pt0) cc_final: 0.8328 (pt0) REVERT: D 193 PHE cc_start: 0.9166 (t80) cc_final: 0.8716 (t80) REVERT: D 196 ASN cc_start: 0.8321 (m-40) cc_final: 0.7663 (p0) REVERT: D 278 GLU cc_start: 0.7977 (pm20) cc_final: 0.7596 (pm20) REVERT: D 298 MET cc_start: 0.8805 (ttt) cc_final: 0.8581 (ttt) REVERT: D 464 SER cc_start: 0.9252 (p) cc_final: 0.8861 (t) REVERT: D 527 LYS cc_start: 0.7272 (pttt) cc_final: 0.6701 (mtpp) REVERT: D 576 PHE cc_start: 0.7562 (m-80) cc_final: 0.7196 (t80) REVERT: E 7 SER cc_start: 0.8742 (t) cc_final: 0.8510 (p) REVERT: E 77 ASN cc_start: 0.8605 (t0) cc_final: 0.8047 (t0) REVERT: F 42 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8455 (mttp) outliers start: 33 outliers final: 19 residues processed: 237 average time/residue: 0.3028 time to fit residues: 104.3121 Evaluate side-chains 221 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 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 328 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 89 GLU 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 182 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15630 Z= 0.240 Angle : 0.559 9.231 21212 Z= 0.280 Chirality : 0.044 0.187 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.096 17.232 2100 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.31 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1930 helix: 1.78 (0.38), residues: 202 sheet: 1.40 (0.19), residues: 790 loop : 0.34 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 PHE 0.013 0.001 PHE A 583 TYR 0.015 0.001 TYR F 49 ARG 0.004 0.000 ARG A 218 *********************** 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 256 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8578 (pt0) cc_final: 0.8341 (pt0) REVERT: A 193 PHE cc_start: 0.9218 (t80) cc_final: 0.8937 (t80) REVERT: A 196 ASN cc_start: 0.8344 (m-40) cc_final: 0.7633 (p0) REVERT: A 278 GLU cc_start: 0.7930 (pm20) cc_final: 0.7556 (pm20) REVERT: A 464 SER cc_start: 0.9299 (p) cc_final: 0.8918 (t) REVERT: A 527 LYS cc_start: 0.7238 (pttt) cc_final: 0.6679 (mtpp) REVERT: A 576 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 7 SER cc_start: 0.8755 (t) cc_final: 0.8455 (p) REVERT: B 77 ASN cc_start: 0.8642 (t0) cc_final: 0.8051 (t0) REVERT: C 22 THR cc_start: 0.8654 (p) cc_final: 0.8405 (t) REVERT: C 42 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8489 (mttp) REVERT: D 146 GLN cc_start: 0.8577 (pt0) cc_final: 0.8285 (pt0) REVERT: D 193 PHE cc_start: 0.9209 (t80) cc_final: 0.8958 (t80) REVERT: D 196 ASN cc_start: 0.8342 (m-40) cc_final: 0.7640 (p0) REVERT: D 278 GLU cc_start: 0.7932 (pm20) cc_final: 0.7553 (pm20) REVERT: D 464 SER cc_start: 0.9295 (p) cc_final: 0.8914 (t) REVERT: D 527 LYS cc_start: 0.7237 (pttt) cc_final: 0.6678 (mtpp) REVERT: D 576 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7197 (t80) REVERT: E 7 SER cc_start: 0.8760 (t) cc_final: 0.8471 (p) REVERT: E 46 GLU cc_start: 0.7805 (tt0) cc_final: 0.7603 (tt0) REVERT: E 77 ASN cc_start: 0.8642 (t0) cc_final: 0.8057 (t0) REVERT: F 22 THR cc_start: 0.8673 (p) cc_final: 0.8418 (t) REVERT: F 42 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8489 (mttp) outliers start: 40 outliers final: 26 residues processed: 240 average time/residue: 0.3131 time to fit residues: 107.4054 Evaluate side-chains 235 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 169 ASP 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 576 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 169 ASP 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 576 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 56 optimal weight: 0.0370 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 0.0020 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15630 Z= 0.138 Angle : 0.531 8.579 21212 Z= 0.262 Chirality : 0.043 0.175 2410 Planarity : 0.004 0.046 2704 Dihedral : 3.798 15.276 2100 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.27 % Allowed : 13.12 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1930 helix: 1.86 (0.38), residues: 202 sheet: 1.47 (0.19), residues: 780 loop : 0.44 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.002 0.000 HIS B 99 PHE 0.017 0.001 PHE A 40 TYR 0.011 0.001 TYR C 49 ARG 0.004 0.000 ARG F 24 *********************** 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 247 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9099 (t80) cc_final: 0.8707 (t80) REVERT: A 196 ASN cc_start: 0.8327 (m-40) cc_final: 0.7715 (p0) REVERT: A 464 SER cc_start: 0.9265 (p) cc_final: 0.8863 (t) REVERT: A 527 LYS cc_start: 0.7229 (pttt) cc_final: 0.6706 (mtpp) REVERT: A 576 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7180 (t80) REVERT: B 62 ASP cc_start: 0.8302 (m-30) cc_final: 0.8055 (m-30) REVERT: B 77 ASN cc_start: 0.8568 (t0) cc_final: 0.8018 (t0) REVERT: D 193 PHE cc_start: 0.9089 (t80) cc_final: 0.8646 (t80) REVERT: D 196 ASN cc_start: 0.8241 (m-40) cc_final: 0.7673 (p0) REVERT: D 464 SER cc_start: 0.9264 (p) cc_final: 0.8858 (t) REVERT: D 527 LYS cc_start: 0.7225 (pttt) cc_final: 0.6702 (mtpp) REVERT: D 576 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7184 (t80) REVERT: E 62 ASP cc_start: 0.8253 (m-30) cc_final: 0.8008 (m-30) REVERT: E 77 ASN cc_start: 0.8567 (t0) cc_final: 0.8014 (t0) outliers start: 22 outliers final: 12 residues processed: 237 average time/residue: 0.3053 time to fit residues: 105.0011 Evaluate side-chains 216 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 328 MET 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 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 F residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15630 Z= 0.226 Angle : 0.563 9.246 21212 Z= 0.283 Chirality : 0.044 0.185 2410 Planarity : 0.005 0.046 2704 Dihedral : 3.983 16.548 2100 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.39 % Allowed : 13.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1930 helix: 1.93 (0.38), residues: 202 sheet: 1.47 (0.19), residues: 778 loop : 0.36 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 PHE 0.012 0.001 PHE D 583 TYR 0.014 0.001 TYR F 49 ARG 0.005 0.000 ARG F 24 *********************** 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 224 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9162 (t80) cc_final: 0.8814 (t80) REVERT: A 196 ASN cc_start: 0.8353 (m-40) cc_final: 0.7723 (p0) REVERT: A 278 GLU cc_start: 0.7986 (pm20) cc_final: 0.7734 (pm20) REVERT: A 464 SER cc_start: 0.9290 (p) cc_final: 0.8921 (t) REVERT: A 527 LYS cc_start: 0.7239 (pttt) cc_final: 0.6739 (mtpp) REVERT: A 576 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7187 (t80) REVERT: B 62 ASP cc_start: 0.8313 (m-30) cc_final: 0.8026 (m-30) REVERT: B 77 ASN cc_start: 0.8622 (t0) cc_final: 0.8176 (t0) REVERT: B 153 TYR cc_start: 0.8132 (p90) cc_final: 0.7641 (p90) REVERT: C 22 THR cc_start: 0.8617 (p) cc_final: 0.8415 (t) REVERT: D 193 PHE cc_start: 0.9134 (t80) cc_final: 0.8755 (t80) REVERT: D 196 ASN cc_start: 0.8372 (m-40) cc_final: 0.7751 (p0) REVERT: D 278 GLU cc_start: 0.7976 (pm20) cc_final: 0.7727 (pm20) REVERT: D 464 SER cc_start: 0.9288 (p) cc_final: 0.8914 (t) REVERT: D 527 LYS cc_start: 0.7238 (pttt) cc_final: 0.6738 (mtpp) REVERT: D 576 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7195 (t80) REVERT: E 77 ASN cc_start: 0.8618 (t0) cc_final: 0.8169 (t0) REVERT: E 153 TYR cc_start: 0.8148 (p90) cc_final: 0.7739 (p90) REVERT: F 22 THR cc_start: 0.8636 (p) cc_final: 0.8435 (t) outliers start: 24 outliers final: 22 residues processed: 215 average time/residue: 0.3000 time to fit residues: 93.8916 Evaluate side-chains 218 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 21 LEU 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 576 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain E residue 37 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 115 optimal weight: 0.0570 chunk 186 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15630 Z= 0.228 Angle : 0.565 9.301 21212 Z= 0.284 Chirality : 0.044 0.186 2410 Planarity : 0.005 0.046 2704 Dihedral : 4.065 18.076 2100 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.39 % Allowed : 13.29 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1930 helix: 1.88 (0.38), residues: 202 sheet: 1.43 (0.19), residues: 778 loop : 0.29 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.004 0.001 HIS D 236 PHE 0.018 0.001 PHE D 40 TYR 0.015 0.001 TYR F 49 ARG 0.005 0.000 ARG F 24 ********************** 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 224 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8421 (m-40) cc_final: 0.7808 (p0) REVERT: A 278 GLU cc_start: 0.7964 (pm20) cc_final: 0.7712 (pm20) REVERT: A 527 LYS cc_start: 0.7240 (pttt) cc_final: 0.6693 (mtpp) REVERT: A 576 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7210 (t80) REVERT: B 62 ASP cc_start: 0.8340 (m-30) cc_final: 0.8107 (p0) REVERT: B 77 ASN cc_start: 0.8624 (t0) cc_final: 0.8182 (t0) REVERT: B 153 TYR cc_start: 0.8200 (p90) cc_final: 0.7685 (p90) REVERT: C 22 THR cc_start: 0.8640 (p) cc_final: 0.8415 (t) REVERT: D 188 LYS cc_start: 0.7678 (tttt) cc_final: 0.7177 (ttpt) REVERT: D 196 ASN cc_start: 0.8429 (m-40) cc_final: 0.7810 (p0) REVERT: D 278 GLU cc_start: 0.7936 (pm20) cc_final: 0.7686 (pm20) REVERT: D 527 LYS cc_start: 0.7238 (pttt) cc_final: 0.6689 (mtpp) REVERT: D 576 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7219 (t80) REVERT: E 77 ASN cc_start: 0.8625 (t0) cc_final: 0.8180 (t0) REVERT: E 153 TYR cc_start: 0.8167 (p90) cc_final: 0.7785 (p90) REVERT: F 22 THR cc_start: 0.8663 (p) cc_final: 0.8430 (t) outliers start: 24 outliers final: 22 residues processed: 215 average time/residue: 0.3122 time to fit residues: 97.1615 Evaluate side-chains 217 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 21 LEU 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 576 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain E residue 37 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 123 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 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 = 0.4090 r_free = 0.4090 target = 0.169818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123187 restraints weight = 23430.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126464 restraints weight = 11684.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127292 restraints weight = 7712.341| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15630 Z= 0.215 Angle : 0.558 9.183 21212 Z= 0.281 Chirality : 0.044 0.184 2410 Planarity : 0.005 0.046 2704 Dihedral : 4.028 17.874 2100 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 13.47 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1930 helix: 1.87 (0.38), residues: 202 sheet: 1.44 (0.19), residues: 778 loop : 0.27 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.004 0.001 HIS D 236 PHE 0.018 0.001 PHE D 40 TYR 0.015 0.001 TYR F 49 ARG 0.005 0.000 ARG F 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.60 seconds wall clock time: 63 minutes 39.08 seconds (3819.08 seconds total)