Starting phenix.real_space_refine on Tue Apr 9 04:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/04_2024/8smk_40589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/04_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_40589/04_2024/8smk_40589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/04_2024/8smk_40589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/04_2024/8smk_40589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smk_40589/04_2024/8smk_40589.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15298 Number of models: 1 Model: "" Number of chains: 8 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: "D" 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: "E" 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: "F" 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} Chain: "D" 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} Time building chain proxies: 8.13, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.9 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 44 sheets defined 15.3% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 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: 6.26 Time building geometry restraints manager: 5.49 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: 98.40 - 105.66: 535 105.66 - 112.92: 7968 112.92 - 120.18: 6294 120.18 - 127.44: 6287 127.44 - 134.69: 128 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 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: 3.800 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: 13.340 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 42.580 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.080 ------------------------------------------------------------------------------- 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= 0.749 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 : 2.054 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1930 helix: 0.55 (0.36), residues: 180 sheet: 1.12 (0.19), residues: 690 loop : 0.86 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP A 466 HIS 0.002 0.000 HIS C 199 PHE 0.039 0.003 PHE D 487 TYR 0.107 0.003 TYR E 105 ARG 0.009 0.001 ARG D 427 *********************** 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 fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 1.627 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: 0.3075 time to fit residues: 198.6142 Evaluate side-chains 270 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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: 4.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 286 GLN A 471 HIS ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 286 GLN D 471 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15630 Z= 0.232 Angle : 0.579 6.738 21212 Z= 0.305 Chirality : 0.045 0.154 2410 Planarity : 0.005 0.054 2704 Dihedral : 4.387 20.634 2100 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.69 (0.20), residues: 1930 helix: 1.81 (0.38), residues: 182 sheet: 1.31 (0.19), residues: 768 loop : 0.99 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 141 HIS 0.005 0.001 HIS D 245 PHE 0.015 0.002 PHE A 407 TYR 0.018 0.002 TYR F 141 ARG 0.004 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 316 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 286 time to evaluate : 1.751 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 45 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8364 (m) REVERT: A 193 PHE cc_start: 0.9207 (t80) cc_final: 0.8823 (t80) REVERT: A 196 ASN cc_start: 0.8062 (m-40) cc_final: 0.7368 (p0) REVERT: A 247 MET cc_start: 0.8075 (tpt) cc_final: 0.7873 (tpt) REVERT: A 276 ASN cc_start: 0.8414 (t0) cc_final: 0.7578 (t0) REVERT: A 352 MET cc_start: 0.7561 (mtt) cc_final: 0.7290 (mtt) REVERT: A 407 PHE cc_start: 0.7604 (m-10) cc_final: 0.7334 (m-80) REVERT: A 474 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7866 (mt-10) REVERT: A 527 LYS cc_start: 0.6908 (pttt) cc_final: 0.6314 (mtpp) REVERT: A 554 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8388 (mtpt) REVERT: B 77 ASN cc_start: 0.8652 (t0) cc_final: 0.8289 (t0) REVERT: C 22 THR cc_start: 0.8511 (p) cc_final: 0.8206 (t) REVERT: C 140 PHE cc_start: 0.8216 (p90) cc_final: 0.7899 (p90) REVERT: C 167 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7768 (tm-30) REVERT: D 45 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8358 (m) REVERT: D 193 PHE cc_start: 0.9208 (t80) cc_final: 0.8824 (t80) REVERT: D 196 ASN cc_start: 0.8059 (m-40) cc_final: 0.7371 (p0) REVERT: D 276 ASN cc_start: 0.8415 (t0) cc_final: 0.7574 (t0) REVERT: D 352 MET cc_start: 0.7565 (mtt) cc_final: 0.7297 (mtt) REVERT: D 407 PHE cc_start: 0.7597 (m-10) cc_final: 0.7329 (m-80) REVERT: D 474 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7858 (mt-10) REVERT: D 527 LYS cc_start: 0.6908 (pttt) cc_final: 0.6315 (mtpp) REVERT: D 554 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8382 (mtpt) REVERT: E 77 ASN cc_start: 0.8650 (t0) cc_final: 0.8286 (t0) REVERT: F 22 THR cc_start: 0.8531 (p) cc_final: 0.8221 (t) REVERT: F 140 PHE cc_start: 0.8237 (p90) cc_final: 0.7733 (p90) REVERT: F 167 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7779 (tm-30) REVERT: F 177 SER cc_start: 0.8182 (t) cc_final: 0.7870 (p) REVERT: F 178 SER cc_start: 0.8219 (t) cc_final: 0.7978 (p) outliers start: 30 outliers final: 20 residues processed: 308 average time/residue: 0.2979 time to fit residues: 131.7346 Evaluate side-chains 243 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 335 THR 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 45 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 335 THR 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 98 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3759 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= 0.251 Angle : 0.564 8.729 21212 Z= 0.292 Chirality : 0.044 0.147 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.227 17.200 2100 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 8.73 % Favored : 88.61 % 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: 1.46 (0.20), residues: 1930 helix: 1.70 (0.38), residues: 186 sheet: 1.26 (0.19), residues: 798 loop : 0.69 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 141 HIS 0.005 0.001 HIS D 236 PHE 0.015 0.001 PHE D 583 TYR 0.021 0.002 TYR B 153 ARG 0.002 0.000 ARG D 495 *********************** 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 283 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9215 (t80) cc_final: 0.8757 (t80) REVERT: A 196 ASN cc_start: 0.8046 (m-40) cc_final: 0.7366 (p0) REVERT: A 352 MET cc_start: 0.7804 (mtt) cc_final: 0.7580 (mtt) REVERT: A 464 SER cc_start: 0.9239 (p) cc_final: 0.8845 (t) REVERT: A 484 ARG cc_start: 0.7919 (ptt-90) cc_final: 0.7432 (ptt90) REVERT: A 527 LYS cc_start: 0.7023 (pttt) cc_final: 0.6438 (mtpp) REVERT: A 543 GLU cc_start: 0.7920 (tt0) cc_final: 0.7669 (tt0) REVERT: A 554 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (mtpt) REVERT: B 77 ASN cc_start: 0.8599 (t0) cc_final: 0.8172 (p0) REVERT: C 167 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7775 (tm-30) REVERT: D 193 PHE cc_start: 0.9216 (t80) cc_final: 0.8758 (t80) REVERT: D 196 ASN cc_start: 0.8049 (m-40) cc_final: 0.7371 (p0) REVERT: D 352 MET cc_start: 0.7804 (mtt) cc_final: 0.7582 (mtt) REVERT: D 464 SER cc_start: 0.9230 (p) cc_final: 0.8830 (t) REVERT: D 484 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7441 (ptt90) REVERT: D 527 LYS cc_start: 0.7014 (pttt) cc_final: 0.6427 (mtpp) REVERT: D 554 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: E 77 ASN cc_start: 0.8598 (t0) cc_final: 0.8173 (p0) REVERT: F 167 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7842 (tm-30) outliers start: 46 outliers final: 26 residues processed: 265 average time/residue: 0.3109 time to fit residues: 117.5380 Evaluate side-chains 224 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 181 SER 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 554 LYS Chi-restraints excluded: chain A residue 661 MET 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 181 SER 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 554 LYS Chi-restraints excluded: chain D residue 661 MET 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 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: 4.9990 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 0.0270 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15630 Z= 0.211 Angle : 0.536 7.966 21212 Z= 0.273 Chirality : 0.043 0.188 2410 Planarity : 0.005 0.043 2704 Dihedral : 4.059 15.200 2100 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.37 % Allowed : 10.69 % Favored : 86.94 % 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: 1.41 (0.20), residues: 1930 helix: 1.31 (0.38), residues: 204 sheet: 1.37 (0.18), residues: 814 loop : 0.56 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 PHE 0.011 0.001 PHE A 583 TYR 0.014 0.001 TYR F 49 ARG 0.002 0.000 ARG F 66 *********************** 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 273 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8555 (pt0) cc_final: 0.8312 (pt0) REVERT: A 175 GLU cc_start: 0.8569 (mp0) cc_final: 0.8332 (pm20) REVERT: A 193 PHE cc_start: 0.9183 (t80) cc_final: 0.8874 (t80) REVERT: A 196 ASN cc_start: 0.8051 (m-40) cc_final: 0.7384 (p0) REVERT: A 352 MET cc_start: 0.7697 (mtt) cc_final: 0.7418 (mtt) REVERT: A 464 SER cc_start: 0.9242 (p) cc_final: 0.8843 (t) REVERT: A 484 ARG cc_start: 0.7942 (ptt-90) cc_final: 0.7446 (ptt90) REVERT: A 527 LYS cc_start: 0.7149 (pttt) cc_final: 0.6579 (mtpp) REVERT: A 554 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8543 (mtpt) REVERT: B 77 ASN cc_start: 0.8559 (t0) cc_final: 0.8176 (p0) REVERT: B 89 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: C 22 THR cc_start: 0.8557 (p) cc_final: 0.8310 (t) REVERT: C 167 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 146 GLN cc_start: 0.8553 (pt0) cc_final: 0.8315 (pt0) REVERT: D 175 GLU cc_start: 0.8570 (mp0) cc_final: 0.8336 (pm20) REVERT: D 193 PHE cc_start: 0.9188 (t80) cc_final: 0.8878 (t80) REVERT: D 196 ASN cc_start: 0.8059 (m-40) cc_final: 0.7393 (p0) REVERT: D 352 MET cc_start: 0.7700 (mtt) cc_final: 0.7430 (mtt) REVERT: D 464 SER cc_start: 0.9235 (p) cc_final: 0.8832 (t) REVERT: D 484 ARG cc_start: 0.7947 (ptt-90) cc_final: 0.7449 (ptt90) REVERT: D 527 LYS cc_start: 0.7149 (pttt) cc_final: 0.6578 (mtpp) REVERT: D 554 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8542 (mtpt) REVERT: E 77 ASN cc_start: 0.8557 (t0) cc_final: 0.8179 (p0) REVERT: F 22 THR cc_start: 0.8576 (p) cc_final: 0.8326 (t) REVERT: F 167 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7768 (tm-30) outliers start: 41 outliers final: 23 residues processed: 260 average time/residue: 0.3294 time to fit residues: 120.5154 Evaluate side-chains 228 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 554 LYS Chi-restraints excluded: chain A residue 596 LEU 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 B residue 178 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP 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 554 LYS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15630 Z= 0.441 Angle : 0.646 10.135 21212 Z= 0.333 Chirality : 0.047 0.200 2410 Planarity : 0.005 0.046 2704 Dihedral : 4.704 19.770 2100 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.47 % Allowed : 10.40 % Favored : 86.13 % 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: 1.02 (0.19), residues: 1930 helix: 1.10 (0.37), residues: 198 sheet: 1.20 (0.18), residues: 798 loop : 0.20 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 141 HIS 0.007 0.001 HIS A 236 PHE 0.019 0.002 PHE A 583 TYR 0.022 0.002 TYR E 105 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 283 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: A 196 ASN cc_start: 0.8194 (m-40) cc_final: 0.7543 (p0) REVERT: A 464 SER cc_start: 0.9294 (p) cc_final: 0.8874 (t) REVERT: A 527 LYS cc_start: 0.7315 (pttt) cc_final: 0.6716 (mtpp) REVERT: A 554 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8567 (mtpt) REVERT: B 77 ASN cc_start: 0.8673 (t0) cc_final: 0.8372 (p0) REVERT: B 89 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: C 17 ASP cc_start: 0.8460 (t0) cc_final: 0.8197 (t0) REVERT: C 137 LEU cc_start: 0.8552 (mm) cc_final: 0.8227 (mp) REVERT: C 167 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 175 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: D 196 ASN cc_start: 0.8194 (m-40) cc_final: 0.7549 (p0) REVERT: D 464 SER cc_start: 0.9294 (p) cc_final: 0.8866 (t) REVERT: D 503 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7658 (tm-30) REVERT: D 527 LYS cc_start: 0.7315 (pttt) cc_final: 0.6717 (mtpp) REVERT: D 554 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8562 (mtpt) REVERT: E 77 ASN cc_start: 0.8673 (t0) cc_final: 0.8375 (p0) REVERT: F 17 ASP cc_start: 0.8462 (t0) cc_final: 0.8200 (t0) REVERT: F 167 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7747 (tm-30) outliers start: 60 outliers final: 43 residues processed: 261 average time/residue: 0.2973 time to fit residues: 111.5993 Evaluate side-chains 246 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 118 CYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 175 GLU 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 328 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 389 PHE 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 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP 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 118 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 175 GLU 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 274 THR Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 389 PHE 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 E residue 102 ARG Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 ASP 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: 1.9990 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 0.0370 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.4646 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= 0.179 Angle : 0.538 8.381 21212 Z= 0.272 Chirality : 0.043 0.191 2410 Planarity : 0.004 0.045 2704 Dihedral : 4.148 17.195 2100 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.37 % Allowed : 12.08 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1930 helix: 1.26 (0.37), residues: 202 sheet: 1.38 (0.18), residues: 806 loop : 0.36 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS D 236 PHE 0.016 0.001 PHE A 40 TYR 0.014 0.001 TYR B 80 ARG 0.004 0.000 ARG A 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 264 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8230 (m-40) cc_final: 0.7637 (p0) REVERT: A 461 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8310 (ttmt) REVERT: A 464 SER cc_start: 0.9269 (p) cc_final: 0.8857 (t) REVERT: A 484 ARG cc_start: 0.7814 (ptt-90) cc_final: 0.7300 (ptt90) REVERT: A 527 LYS cc_start: 0.7226 (pttt) cc_final: 0.6639 (mtpp) REVERT: A 554 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8609 (mtpt) REVERT: A 576 PHE cc_start: 0.7629 (m-80) cc_final: 0.7227 (t80) REVERT: B 77 ASN cc_start: 0.8606 (t0) cc_final: 0.8214 (t0) REVERT: B 89 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: C 17 ASP cc_start: 0.8364 (t0) cc_final: 0.8103 (t0) REVERT: C 22 THR cc_start: 0.8623 (p) cc_final: 0.8357 (t) REVERT: C 42 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8471 (mttp) REVERT: C 88 CYS cc_start: 0.8294 (t) cc_final: 0.8091 (t) REVERT: D 196 ASN cc_start: 0.8229 (m-40) cc_final: 0.7643 (p0) REVERT: D 215 GLN cc_start: 0.7997 (tt0) cc_final: 0.7780 (tt0) REVERT: D 461 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8327 (ttmt) REVERT: D 464 SER cc_start: 0.9270 (p) cc_final: 0.8849 (t) REVERT: D 484 ARG cc_start: 0.7823 (ptt-90) cc_final: 0.7306 (ptt90) REVERT: D 527 LYS cc_start: 0.7225 (pttt) cc_final: 0.6640 (mtpp) REVERT: D 554 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: D 576 PHE cc_start: 0.7633 (m-80) cc_final: 0.7237 (t80) REVERT: E 77 ASN cc_start: 0.8609 (t0) cc_final: 0.8214 (t0) REVERT: F 17 ASP cc_start: 0.8368 (t0) cc_final: 0.8106 (t0) REVERT: F 22 THR cc_start: 0.8642 (p) cc_final: 0.8372 (t) REVERT: F 42 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8475 (mttp) outliers start: 41 outliers final: 23 residues processed: 250 average time/residue: 0.3092 time to fit residues: 111.3154 Evaluate side-chains 234 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 554 LYS 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 B residue 178 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 ASP 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: 0.8980 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 115 optimal weight: 0.0040 chunk 87 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.4808 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= 0.165 Angle : 0.518 8.229 21212 Z= 0.259 Chirality : 0.043 0.185 2410 Planarity : 0.004 0.044 2704 Dihedral : 3.929 16.396 2100 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.54 % Allowed : 11.10 % 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 (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: 1.58 (0.38), residues: 202 sheet: 1.44 (0.18), residues: 796 loop : 0.46 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 466 HIS 0.003 0.001 HIS D 236 PHE 0.008 0.001 PHE A 583 TYR 0.013 0.001 TYR E 80 ARG 0.004 0.000 ARG D 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 282 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8163 (m-40) cc_final: 0.7583 (p0) REVERT: A 321 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6951 (mmtt) REVERT: A 461 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8327 (ttmt) REVERT: A 464 SER cc_start: 0.9265 (p) cc_final: 0.8828 (t) REVERT: A 527 LYS cc_start: 0.7295 (pttt) cc_final: 0.6739 (mtpp) REVERT: A 576 PHE cc_start: 0.7626 (m-80) cc_final: 0.7232 (t80) REVERT: B 7 SER cc_start: 0.8778 (t) cc_final: 0.8569 (p) REVERT: B 89 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: C 17 ASP cc_start: 0.8332 (t0) cc_final: 0.8051 (t0) REVERT: C 42 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8484 (mttp) REVERT: D 196 ASN cc_start: 0.8160 (m-40) cc_final: 0.7590 (p0) REVERT: D 321 LYS cc_start: 0.7297 (mmtt) cc_final: 0.6957 (mmtt) REVERT: D 461 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8337 (ttmt) REVERT: D 464 SER cc_start: 0.9269 (p) cc_final: 0.8826 (t) REVERT: D 527 LYS cc_start: 0.7321 (pttt) cc_final: 0.6764 (mtpp) REVERT: D 576 PHE cc_start: 0.7633 (m-80) cc_final: 0.7241 (t80) REVERT: F 17 ASP cc_start: 0.8334 (t0) cc_final: 0.8055 (t0) REVERT: F 22 THR cc_start: 0.8603 (p) cc_final: 0.8378 (t) REVERT: F 42 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8486 (mttp) outliers start: 44 outliers final: 31 residues processed: 267 average time/residue: 0.3010 time to fit residues: 115.9105 Evaluate side-chains 246 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 195 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 195 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 274 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.0470 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 17 optimal weight: 0.0170 chunk 148 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15630 Z= 0.153 Angle : 0.524 8.967 21212 Z= 0.262 Chirality : 0.043 0.186 2410 Planarity : 0.004 0.043 2704 Dihedral : 3.854 16.071 2100 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.72 % Allowed : 11.97 % 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: 1.47 (0.20), residues: 1930 helix: 1.72 (0.38), residues: 202 sheet: 1.50 (0.18), residues: 798 loop : 0.42 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 466 HIS 0.002 0.000 HIS D 236 PHE 0.016 0.001 PHE A 40 TYR 0.012 0.001 TYR B 80 ARG 0.003 0.000 ARG A 218 *********************** 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 266 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8145 (m-40) cc_final: 0.7610 (p0) REVERT: A 321 LYS cc_start: 0.7374 (mmtt) cc_final: 0.7072 (mmtt) REVERT: A 461 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8327 (ttmt) REVERT: A 464 SER cc_start: 0.9266 (p) cc_final: 0.8848 (t) REVERT: A 527 LYS cc_start: 0.7259 (pttt) cc_final: 0.6728 (mtpp) REVERT: A 576 PHE cc_start: 0.7620 (m-80) cc_final: 0.7217 (t80) REVERT: B 7 SER cc_start: 0.8822 (t) cc_final: 0.8586 (p) REVERT: C 17 ASP cc_start: 0.8309 (t0) cc_final: 0.8015 (t0) REVERT: C 42 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8487 (mttp) REVERT: D 196 ASN cc_start: 0.8139 (m-40) cc_final: 0.7606 (p0) REVERT: D 321 LYS cc_start: 0.7381 (mmtt) cc_final: 0.7079 (mmtt) REVERT: D 461 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8338 (ttmt) REVERT: D 464 SER cc_start: 0.9275 (p) cc_final: 0.8847 (t) REVERT: D 527 LYS cc_start: 0.7270 (pttt) cc_final: 0.6743 (mtpp) REVERT: D 576 PHE cc_start: 0.7627 (m-80) cc_final: 0.7229 (t80) REVERT: E 7 SER cc_start: 0.8827 (t) cc_final: 0.8603 (p) REVERT: F 17 ASP cc_start: 0.8317 (t0) cc_final: 0.8021 (t0) REVERT: F 42 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8489 (mttp) outliers start: 47 outliers final: 33 residues processed: 250 average time/residue: 0.2942 time to fit residues: 107.3227 Evaluate side-chains 235 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 111 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 CYS 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 274 THR Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 LEU 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: 4.9990 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS D 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 15630 Z= 0.568 Angle : 0.711 10.913 21212 Z= 0.365 Chirality : 0.049 0.211 2410 Planarity : 0.005 0.044 2704 Dihedral : 4.834 22.584 2100 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 12.02 % 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: 0.73 (0.19), residues: 1930 helix: 1.06 (0.37), residues: 202 sheet: 1.06 (0.18), residues: 796 loop : -0.10 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 141 HIS 0.008 0.002 HIS A 236 PHE 0.023 0.002 PHE A 583 TYR 0.027 0.002 TYR B 105 ARG 0.005 0.001 ARG D 495 *********************** 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 249 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8363 (m-40) cc_final: 0.7719 (p0) REVERT: A 321 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7068 (mmtt) REVERT: A 461 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8314 (ttmt) REVERT: A 464 SER cc_start: 0.9401 (p) cc_final: 0.9031 (t) REVERT: A 503 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 527 LYS cc_start: 0.7394 (pttt) cc_final: 0.6879 (mtpp) REVERT: C 17 ASP cc_start: 0.8478 (t0) cc_final: 0.8171 (t0) REVERT: D 196 ASN cc_start: 0.8362 (m-40) cc_final: 0.7720 (p0) REVERT: D 321 LYS cc_start: 0.7315 (mmtt) cc_final: 0.7072 (mmtt) REVERT: D 461 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8315 (ttmt) REVERT: D 464 SER cc_start: 0.9398 (p) cc_final: 0.9028 (t) REVERT: D 503 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 527 LYS cc_start: 0.7398 (pttt) cc_final: 0.6883 (mtpp) REVERT: F 17 ASP cc_start: 0.8484 (t0) cc_final: 0.8175 (t0) outliers start: 50 outliers final: 47 residues processed: 233 average time/residue: 0.3138 time to fit residues: 104.1274 Evaluate side-chains 243 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 111 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP 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 111 THR Chi-restraints excluded: chain D residue 118 CYS 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 274 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 163 ASN 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 82 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 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: 0.8109 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15630 Z= 0.226 Angle : 0.571 9.190 21212 Z= 0.288 Chirality : 0.044 0.202 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.331 19.369 2100 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.79 % Allowed : 13.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1930 helix: 1.30 (0.38), residues: 202 sheet: 1.16 (0.19), residues: 800 loop : 0.08 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 162 HIS 0.003 0.001 HIS A 236 PHE 0.020 0.001 PHE A 40 TYR 0.016 0.001 TYR F 49 ARG 0.003 0.000 ARG D 218 ********************** 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 246 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8308 (ttm) cc_final: 0.8085 (ttp) REVERT: A 196 ASN cc_start: 0.8281 (m-40) cc_final: 0.7673 (p0) REVERT: A 321 LYS cc_start: 0.7261 (mmtt) cc_final: 0.7031 (mmtt) REVERT: A 464 SER cc_start: 0.9354 (p) cc_final: 0.8956 (t) REVERT: A 527 LYS cc_start: 0.7315 (pttt) cc_final: 0.6759 (mtpp) REVERT: B 7 SER cc_start: 0.8721 (t) cc_final: 0.8519 (p) REVERT: C 17 ASP cc_start: 0.8441 (t0) cc_final: 0.8133 (t0) REVERT: C 22 THR cc_start: 0.8600 (p) cc_final: 0.8344 (t) REVERT: C 42 LYS cc_start: 0.8796 (mmtp) cc_final: 0.8486 (mttp) REVERT: D 164 MET cc_start: 0.8310 (ttm) cc_final: 0.8087 (ttp) REVERT: D 196 ASN cc_start: 0.8279 (m-40) cc_final: 0.7674 (p0) REVERT: D 215 GLN cc_start: 0.8068 (tt0) cc_final: 0.7828 (tt0) REVERT: D 321 LYS cc_start: 0.7266 (mmtt) cc_final: 0.7038 (mmtt) REVERT: D 464 SER cc_start: 0.9328 (p) cc_final: 0.8927 (t) REVERT: D 527 LYS cc_start: 0.7314 (pttt) cc_final: 0.6758 (mtpp) REVERT: F 17 ASP cc_start: 0.8448 (t0) cc_final: 0.8138 (t0) REVERT: F 22 THR cc_start: 0.8614 (p) cc_final: 0.8359 (t) REVERT: F 42 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8491 (mttp) outliers start: 31 outliers final: 29 residues processed: 236 average time/residue: 0.3100 time to fit residues: 104.9690 Evaluate side-chains 235 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.167478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120198 restraints weight = 23587.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121458 restraints weight = 11978.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123325 restraints weight = 8699.829| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15630 Z= 0.275 Angle : 0.574 9.644 21212 Z= 0.292 Chirality : 0.045 0.198 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.317 19.342 2100 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.25 % Allowed : 13.01 % Favored : 84.74 % 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: 0.92 (0.20), residues: 1930 helix: 1.28 (0.38), residues: 202 sheet: 1.14 (0.19), residues: 800 loop : 0.05 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 149 HIS 0.005 0.001 HIS D 236 PHE 0.012 0.001 PHE A 583 TYR 0.018 0.001 TYR F 49 ARG 0.003 0.000 ARG D 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.75 seconds wall clock time: 63 minutes 40.95 seconds (3820.95 seconds total)