Starting phenix.real_space_refine on Mon Mar 11 18:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/03_2024/7jyi_22526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/03_2024/7jyi_22526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/03_2024/7jyi_22526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/03_2024/7jyi_22526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/03_2024/7jyi_22526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/03_2024/7jyi_22526.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5586 2.51 5 N 1512 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ASP 426": "OD1" <-> "OD2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "E PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 189": "OD1" <-> "OD2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E GLU 274": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E ASP 296": "OD1" <-> "OD2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E ASP 426": "OD1" <-> "OD2" Residue "E PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 33": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8807 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3799 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3799 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 605 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 5.22, per 1000 atoms: 0.59 Number of scatterers: 8807 At special positions: 0 Unit cell: (104.5, 158.4, 81.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1647 8.00 N 1512 7.00 C 5586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.29 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.29 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 24 sheets defined 26.6% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.931A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.556A pdb=" N ILE C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 removed outlier: 3.535A pdb=" N ASP C 200 " --> pdb=" O ASP C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.765A pdb=" N ALA C 241 " --> pdb=" O ASN C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.521A pdb=" N ALA C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 270 " --> pdb=" O HIS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.008A pdb=" N PHE C 431 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 461 through 478 Processing helix chain 'C' and resid 484 through 496 removed outlier: 3.914A pdb=" N LEU C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 removed outlier: 4.264A pdb=" N TYR D 25 " --> pdb=" O SER D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.628A pdb=" N LYS D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.905A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.874A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.931A pdb=" N SER E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.556A pdb=" N ILE E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 200 removed outlier: 3.535A pdb=" N ASP E 200 " --> pdb=" O ASP E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.765A pdb=" N ALA E 241 " --> pdb=" O ASN E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 261 through 270 removed outlier: 3.520A pdb=" N ALA E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA E 270 " --> pdb=" O HIS E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 425 Processing helix chain 'E' and resid 426 through 431 removed outlier: 4.008A pdb=" N PHE E 431 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 455 Processing helix chain 'E' and resid 461 through 478 Processing helix chain 'E' and resid 484 through 496 removed outlier: 3.914A pdb=" N LEU E 491 " --> pdb=" O THR E 487 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL E 494 " --> pdb=" O ALA E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 41 through 54 removed outlier: 3.750A pdb=" N VAL F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 71 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.559A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 138 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.559A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.663A pdb=" N ARG C 292 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 90 through 95 removed outlier: 8.966A pdb=" N LEU C 113 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER C 70 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR C 115 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET C 68 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA C 117 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER C 66 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE C 119 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 64 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS C 121 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU C 62 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS C 123 " --> pdb=" O CYS C 60 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS C 60 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N MET C 125 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 58 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C 54 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 58 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.279A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 273 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AA7, first strand: chain 'C' and resid 243 through 247 Processing sheet with id=AA8, first strand: chain 'C' and resid 319 through 320 removed outlier: 3.641A pdb=" N ALA C 319 " --> pdb=" O THR C 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.580A pdb=" N SER C 372 " --> pdb=" O TYR C 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.752A pdb=" N ARG C 357 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.558A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG E 138 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR E 48 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.558A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.663A pdb=" N ARG E 292 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 95 removed outlier: 8.966A pdb=" N LEU E 113 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER E 70 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N THR E 115 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET E 68 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA E 117 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER E 66 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE E 119 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER E 64 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N CYS E 121 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU E 62 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS E 123 " --> pdb=" O CYS E 60 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N CYS E 60 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N MET E 125 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER E 58 " --> pdb=" O MET E 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY E 127 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA E 54 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E 58 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 95 removed outlier: 4.279A pdb=" N HIS E 210 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU E 273 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 Processing sheet with id=AC1, first strand: chain 'E' and resid 243 through 247 Processing sheet with id=AC2, first strand: chain 'E' and resid 319 through 320 removed outlier: 3.642A pdb=" N ALA E 319 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 329 through 333 removed outlier: 3.581A pdb=" N SER E 372 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AC5, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AC6, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.752A pdb=" N ARG E 357 " --> pdb=" O ASP E 379 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 1666 1.46 - 1.57: 4384 1.57 - 1.69: 0 1.69 - 1.80: 98 Bond restraints: 8999 Sorted by residual: bond pdb=" CA TYR F 74 " pdb=" C TYR F 74 " ideal model delta sigma weight residual 1.532 1.516 0.016 9.60e-03 1.09e+04 2.77e+00 bond pdb=" CA THR E 479 " pdb=" CB THR E 479 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.51e-02 4.39e+03 2.31e+00 bond pdb=" CA THR C 479 " pdb=" CB THR C 479 " ideal model delta sigma weight residual 1.532 1.553 -0.021 1.48e-02 4.57e+03 2.07e+00 bond pdb=" CB VAL C 265 " pdb=" CG1 VAL C 265 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CB VAL E 265 " pdb=" CG1 VAL E 265 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 ... (remaining 8994 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.41: 150 105.41 - 112.61: 4940 112.61 - 119.81: 2825 119.81 - 127.00: 4147 127.00 - 134.20: 134 Bond angle restraints: 12196 Sorted by residual: angle pdb=" C LEU E 498 " pdb=" N SER E 499 " pdb=" CA SER E 499 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C LEU C 498 " pdb=" N SER C 499 " pdb=" CA SER C 499 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" CA THR E 479 " pdb=" CB THR E 479 " pdb=" CG2 THR E 479 " ideal model delta sigma weight residual 110.50 118.42 -7.92 1.70e+00 3.46e-01 2.17e+01 angle pdb=" CA THR C 479 " pdb=" CB THR C 479 " pdb=" CG2 THR C 479 " ideal model delta sigma weight residual 110.50 118.40 -7.90 1.70e+00 3.46e-01 2.16e+01 angle pdb=" CA HIS C 249 " pdb=" C HIS C 249 " pdb=" N ALA C 250 " ideal model delta sigma weight residual 119.71 115.25 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4712 17.98 - 35.96: 409 35.96 - 53.94: 132 53.94 - 71.92: 35 71.92 - 89.90: 9 Dihedral angle restraints: 5297 sinusoidal: 2045 harmonic: 3252 Sorted by residual: dihedral pdb=" CA LEU E 498 " pdb=" C LEU E 498 " pdb=" N SER E 499 " pdb=" CA SER E 499 " ideal model delta harmonic sigma weight residual -180.00 -142.62 -37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU C 498 " pdb=" C LEU C 498 " pdb=" N SER C 499 " pdb=" CA SER C 499 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 dihedral pdb=" CA HIS E 226 " pdb=" C HIS E 226 " pdb=" N ALA E 227 " pdb=" CA ALA E 227 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 5294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1064 0.050 - 0.100: 265 0.100 - 0.150: 57 0.150 - 0.200: 0 0.200 - 0.250: 2 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB THR C 479 " pdb=" CA THR C 479 " pdb=" OG1 THR C 479 " pdb=" CG2 THR C 479 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR E 479 " pdb=" CA THR E 479 " pdb=" OG1 THR E 479 " pdb=" CG2 THR E 479 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" C PRO C 132 " pdb=" CB PRO C 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1385 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 498 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C LEU C 498 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU C 498 " 0.023 2.00e-02 2.50e+03 pdb=" N SER C 499 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 498 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU E 498 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU E 498 " -0.023 2.00e-02 2.50e+03 pdb=" N SER E 499 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 2 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ARG C 2 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG C 2 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS C 3 " 0.011 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 232 2.66 - 3.22: 7960 3.22 - 3.78: 12621 3.78 - 4.34: 17677 4.34 - 4.90: 30892 Nonbonded interactions: 69382 Sorted by model distance: nonbonded pdb=" OE2 GLU C 133 " pdb=" NH2 ARG C 193 " model vdw 2.104 2.520 nonbonded pdb=" OE2 GLU E 133 " pdb=" NH2 ARG E 193 " model vdw 2.104 2.520 nonbonded pdb=" O CYS E 488 " pdb=" CG LEU E 491 " model vdw 2.144 3.470 nonbonded pdb=" O CYS C 488 " pdb=" CG LEU C 491 " model vdw 2.146 3.470 nonbonded pdb=" O GLY E 436 " pdb=" OG SER E 440 " model vdw 2.179 2.440 ... (remaining 69377 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 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name OG )))) } 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 individual isotropic 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.270 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.520 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.008 0.047 8999 Z= 0.514 Angle : 0.745 9.778 12196 Z= 0.428 Chirality : 0.046 0.250 1388 Planarity : 0.004 0.035 1537 Dihedral : 16.050 89.897 3209 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.31 % Favored : 89.16 % Rotamer: Outliers : 5.45 % Allowed : 16.14 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.54 (0.20), residues: 1144 helix: -1.77 (0.27), residues: 256 sheet: -2.54 (0.25), residues: 356 loop : -4.03 (0.20), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 400 HIS 0.005 0.001 HIS C 226 PHE 0.024 0.002 PHE E 431 TYR 0.027 0.002 TYR E 158 ARG 0.004 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: C 220 ASP cc_start: 0.7954 (m-30) cc_final: 0.7626 (m-30) REVERT: C 277 MET cc_start: 0.7956 (ttm) cc_final: 0.7604 (ttm) REVERT: C 295 MET cc_start: 0.8285 (ttm) cc_final: 0.7965 (mtp) REVERT: C 332 TYR cc_start: 0.7768 (t80) cc_final: 0.7544 (t80) REVERT: C 400 TRP cc_start: 0.8215 (t-100) cc_final: 0.7470 (t-100) REVERT: C 416 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7275 (mtm110) REVERT: C 449 PHE cc_start: 0.6486 (t80) cc_final: 0.5981 (m-10) REVERT: C 454 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8197 (tmmt) REVERT: D 4 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8723 (mm) REVERT: E 4 ILE cc_start: 0.7977 (tt) cc_final: 0.7756 (mt) REVERT: E 151 MET cc_start: 0.5453 (mmt) cc_final: 0.5241 (mmp) REVERT: E 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7586 (t70) REVERT: F 10 ARG cc_start: 0.9092 (mmt-90) cc_final: 0.8839 (mmt90) outliers start: 52 outliers final: 23 residues processed: 274 average time/residue: 0.2236 time to fit residues: 82.2725 Evaluate side-chains 183 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN C 208 ASN C 219 HIS C 362 ASN D 39 ASN E 85 GLN E 134 ASN E 147 GLN E 208 ASN E 219 HIS E 371 ASN E 439 ASN E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8999 Z= 0.226 Angle : 0.588 9.291 12196 Z= 0.299 Chirality : 0.043 0.160 1388 Planarity : 0.004 0.038 1537 Dihedral : 6.979 72.889 1252 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.00 % Favored : 90.91 % Rotamer: Outliers : 5.14 % Allowed : 18.55 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.54 (0.22), residues: 1144 helix: -0.54 (0.32), residues: 258 sheet: -2.10 (0.25), residues: 370 loop : -3.53 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 462 HIS 0.007 0.001 HIS C 226 PHE 0.014 0.001 PHE C 431 TYR 0.011 0.001 TYR D 74 ARG 0.003 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 332 TYR cc_start: 0.8148 (t80) cc_final: 0.7904 (t80) REVERT: C 400 TRP cc_start: 0.8234 (t-100) cc_final: 0.7985 (t-100) REVERT: C 416 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7313 (mtm110) REVERT: C 449 PHE cc_start: 0.6404 (t80) cc_final: 0.5852 (m-10) REVERT: C 454 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8463 (ttpp) REVERT: C 456 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8672 (mp) REVERT: C 477 LEU cc_start: 0.8759 (mt) cc_final: 0.8482 (mt) REVERT: D 4 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8522 (mm) REVERT: E 377 GLU cc_start: 0.8011 (tt0) cc_final: 0.7680 (tt0) REVERT: E 478 ASN cc_start: 0.8665 (m-40) cc_final: 0.8462 (m110) REVERT: F 10 ARG cc_start: 0.9010 (mmt-90) cc_final: 0.8797 (mmt90) outliers start: 49 outliers final: 27 residues processed: 216 average time/residue: 0.2109 time to fit residues: 62.2978 Evaluate side-chains 185 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN ** E 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8999 Z= 0.168 Angle : 0.540 7.453 12196 Z= 0.274 Chirality : 0.041 0.147 1388 Planarity : 0.003 0.039 1537 Dihedral : 5.358 70.337 1229 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 4.51 % Allowed : 20.23 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.99 (0.23), residues: 1144 helix: 0.04 (0.33), residues: 256 sheet: -1.58 (0.26), residues: 344 loop : -3.36 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 474 HIS 0.007 0.001 HIS C 266 PHE 0.012 0.001 PHE C 431 TYR 0.007 0.001 TYR D 74 ARG 0.004 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 0.992 Fit side-chains REVERT: C 332 TYR cc_start: 0.8188 (t80) cc_final: 0.7958 (t80) REVERT: C 416 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7299 (mtm110) REVERT: C 456 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8341 (mp) REVERT: C 477 LEU cc_start: 0.8795 (mt) cc_final: 0.8431 (mt) REVERT: D 4 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8464 (mm) REVERT: E 66 SER cc_start: 0.8744 (m) cc_final: 0.8482 (t) REVERT: E 94 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7977 (mtt180) REVERT: E 384 ASP cc_start: 0.7014 (p0) cc_final: 0.6716 (p0) REVERT: E 478 ASN cc_start: 0.8642 (m-40) cc_final: 0.8406 (m110) outliers start: 43 outliers final: 33 residues processed: 194 average time/residue: 0.2237 time to fit residues: 59.3283 Evaluate side-chains 182 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN C 401 HIS E 249 HIS E 439 ASN ** E 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 8999 Z= 0.508 Angle : 0.702 11.550 12196 Z= 0.354 Chirality : 0.047 0.152 1388 Planarity : 0.004 0.041 1537 Dihedral : 6.102 89.144 1228 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.70 % Favored : 90.12 % Rotamer: Outliers : 5.56 % Allowed : 21.59 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.97 (0.23), residues: 1144 helix: -0.31 (0.31), residues: 270 sheet: -1.68 (0.25), residues: 386 loop : -3.17 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 20 HIS 0.009 0.002 HIS C 226 PHE 0.026 0.002 PHE C 431 TYR 0.022 0.002 TYR E 61 ARG 0.004 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.6877 (mmt) cc_final: 0.6569 (mmp) REVERT: C 175 ARG cc_start: 0.6724 (ptt-90) cc_final: 0.5980 (ptt-90) REVERT: C 277 MET cc_start: 0.7876 (ttm) cc_final: 0.7651 (ttm) REVERT: C 416 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7323 (ttp80) REVERT: C 449 PHE cc_start: 0.6727 (t80) cc_final: 0.6044 (m-10) REVERT: C 456 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 477 LEU cc_start: 0.8880 (mt) cc_final: 0.8647 (mt) REVERT: D 4 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8599 (mm) REVERT: E 66 SER cc_start: 0.9009 (m) cc_final: 0.8803 (t) REVERT: E 478 ASN cc_start: 0.8669 (m-40) cc_final: 0.8420 (m110) outliers start: 53 outliers final: 41 residues processed: 184 average time/residue: 0.1908 time to fit residues: 49.7585 Evaluate side-chains 186 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN E 447 GLN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8999 Z= 0.198 Angle : 0.571 9.034 12196 Z= 0.286 Chirality : 0.041 0.146 1388 Planarity : 0.003 0.041 1537 Dihedral : 5.595 84.095 1226 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.30 % Favored : 91.61 % Rotamer: Outliers : 4.61 % Allowed : 23.48 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.24), residues: 1144 helix: 0.02 (0.32), residues: 270 sheet: -1.36 (0.27), residues: 358 loop : -2.92 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.007 0.001 HIS C 226 PHE 0.013 0.001 PHE E 431 TYR 0.015 0.001 TYR E 332 ARG 0.003 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.6715 (mmt) cc_final: 0.6477 (mmp) REVERT: C 175 ARG cc_start: 0.6421 (ptt-90) cc_final: 0.5519 (ptt-90) REVERT: C 416 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7307 (ttp80) REVERT: C 449 PHE cc_start: 0.6692 (t80) cc_final: 0.5909 (m-10) REVERT: C 456 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8467 (mp) REVERT: C 477 LEU cc_start: 0.8797 (mt) cc_final: 0.8540 (mt) REVERT: D 4 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8644 (mm) REVERT: E 66 SER cc_start: 0.8989 (m) cc_final: 0.8754 (t) REVERT: E 151 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.4528 (mpp) REVERT: E 345 MET cc_start: 0.8693 (mtp) cc_final: 0.8414 (mtm) REVERT: E 478 ASN cc_start: 0.8608 (m-40) cc_final: 0.8390 (m110) outliers start: 44 outliers final: 33 residues processed: 180 average time/residue: 0.2147 time to fit residues: 54.1557 Evaluate side-chains 181 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8999 Z= 0.517 Angle : 0.720 10.298 12196 Z= 0.360 Chirality : 0.047 0.153 1388 Planarity : 0.004 0.043 1537 Dihedral : 6.109 86.901 1226 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.97 % Favored : 89.86 % Rotamer: Outliers : 5.87 % Allowed : 23.79 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.59 (0.24), residues: 1144 helix: -0.22 (0.32), residues: 270 sheet: -1.33 (0.26), residues: 382 loop : -2.89 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 400 HIS 0.009 0.001 HIS C 226 PHE 0.026 0.002 PHE C 431 TYR 0.026 0.002 TYR E 332 ARG 0.004 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: C 15 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6225 (mtp) REVERT: C 151 MET cc_start: 0.7213 (mmt) cc_final: 0.6918 (mmp) REVERT: C 175 ARG cc_start: 0.6497 (ptt-90) cc_final: 0.5393 (mtm-85) REVERT: C 314 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: C 416 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7306 (ttp80) REVERT: C 449 PHE cc_start: 0.6655 (t80) cc_final: 0.6019 (m-10) REVERT: C 456 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8722 (mp) REVERT: D 4 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8644 (mm) REVERT: E 66 SER cc_start: 0.9044 (m) cc_final: 0.8779 (t) REVERT: E 151 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.4915 (mpp) REVERT: E 478 ASN cc_start: 0.8707 (m-40) cc_final: 0.8474 (m110) outliers start: 56 outliers final: 46 residues processed: 186 average time/residue: 0.1898 time to fit residues: 50.2121 Evaluate side-chains 193 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 142 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8999 Z= 0.164 Angle : 0.557 10.039 12196 Z= 0.279 Chirality : 0.041 0.143 1388 Planarity : 0.003 0.042 1537 Dihedral : 5.527 85.118 1226 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.35 % Allowed : 24.53 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.24), residues: 1144 helix: 0.21 (0.33), residues: 266 sheet: -1.12 (0.27), residues: 342 loop : -2.61 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 19 HIS 0.007 0.001 HIS C 226 PHE 0.010 0.001 PHE E 431 TYR 0.017 0.001 TYR E 332 ARG 0.003 0.000 ARG F 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 150 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.7146 (mmt) cc_final: 0.6863 (mmp) REVERT: C 175 ARG cc_start: 0.6399 (ptt-90) cc_final: 0.5360 (mtm-85) REVERT: C 416 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7281 (ttp80) REVERT: C 449 PHE cc_start: 0.6625 (t80) cc_final: 0.5895 (m-10) REVERT: C 456 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8519 (mp) REVERT: C 478 ASN cc_start: 0.7790 (m110) cc_final: 0.7331 (p0) REVERT: D 4 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8537 (mm) REVERT: E 151 MET cc_start: 0.6164 (OUTLIER) cc_final: 0.4777 (mpp) REVERT: E 345 MET cc_start: 0.8671 (mtp) cc_final: 0.8406 (mtm) outliers start: 51 outliers final: 33 residues processed: 182 average time/residue: 0.1917 time to fit residues: 49.5201 Evaluate side-chains 175 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8999 Z= 0.297 Angle : 0.617 11.039 12196 Z= 0.306 Chirality : 0.042 0.136 1388 Planarity : 0.004 0.041 1537 Dihedral : 5.627 87.571 1225 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.30 % Favored : 91.52 % Rotamer: Outliers : 4.72 % Allowed : 25.68 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.24), residues: 1144 helix: 0.18 (0.33), residues: 268 sheet: -1.04 (0.27), residues: 356 loop : -2.59 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 400 HIS 0.008 0.001 HIS C 226 PHE 0.018 0.001 PHE C 431 TYR 0.020 0.002 TYR E 305 ARG 0.004 0.000 ARG F 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 139 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.7051 (mmt) cc_final: 0.6720 (mmp) REVERT: C 175 ARG cc_start: 0.6406 (ptt-90) cc_final: 0.5335 (mtm-85) REVERT: C 416 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7296 (ttp80) REVERT: C 449 PHE cc_start: 0.6591 (t80) cc_final: 0.5936 (m-10) REVERT: C 456 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8596 (mp) REVERT: D 4 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8576 (mm) REVERT: E 151 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.4941 (mpp) REVERT: E 478 ASN cc_start: 0.8531 (m-40) cc_final: 0.8269 (m-40) outliers start: 45 outliers final: 37 residues processed: 173 average time/residue: 0.1843 time to fit residues: 45.5300 Evaluate side-chains 177 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 484 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0170 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 0.0000 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8999 Z= 0.161 Angle : 0.562 11.202 12196 Z= 0.279 Chirality : 0.040 0.142 1388 Planarity : 0.003 0.042 1537 Dihedral : 5.335 84.512 1225 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.30 % Allowed : 26.00 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.25), residues: 1144 helix: 0.41 (0.33), residues: 268 sheet: -0.85 (0.28), residues: 342 loop : -2.37 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 462 HIS 0.006 0.001 HIS C 226 PHE 0.010 0.001 PHE E 431 TYR 0.017 0.001 TYR E 305 ARG 0.003 0.000 ARG F 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 0.939 Fit side-chains REVERT: C 151 MET cc_start: 0.7071 (mmt) cc_final: 0.6765 (mmp) REVERT: C 175 ARG cc_start: 0.6307 (ptt-90) cc_final: 0.5270 (mtm-85) REVERT: C 416 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7280 (ttp80) REVERT: C 456 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 478 ASN cc_start: 0.7821 (m-40) cc_final: 0.7324 (p0) REVERT: D 4 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8477 (mm) REVERT: E 151 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5369 (mpp) REVERT: E 345 MET cc_start: 0.8677 (mtp) cc_final: 0.8389 (mtm) REVERT: E 478 ASN cc_start: 0.8427 (m-40) cc_final: 0.8123 (m110) outliers start: 41 outliers final: 37 residues processed: 166 average time/residue: 0.2048 time to fit residues: 48.0182 Evaluate side-chains 174 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8999 Z= 0.235 Angle : 0.581 11.159 12196 Z= 0.288 Chirality : 0.041 0.134 1388 Planarity : 0.003 0.042 1537 Dihedral : 5.374 85.275 1223 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 4.19 % Allowed : 26.52 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.25), residues: 1144 helix: 0.45 (0.33), residues: 268 sheet: -0.80 (0.28), residues: 346 loop : -2.35 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 474 HIS 0.007 0.001 HIS C 226 PHE 0.016 0.001 PHE E 431 TYR 0.017 0.001 TYR E 332 ARG 0.004 0.000 ARG F 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.7086 (mmt) cc_final: 0.6823 (mmm) REVERT: C 175 ARG cc_start: 0.6237 (ptt-90) cc_final: 0.5156 (mtm-85) REVERT: C 416 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7296 (ttp80) REVERT: C 449 PHE cc_start: 0.6575 (t80) cc_final: 0.5842 (m-10) REVERT: C 456 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8485 (mp) REVERT: C 478 ASN cc_start: 0.7867 (m-40) cc_final: 0.7368 (p0) REVERT: D 4 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8596 (mm) REVERT: E 151 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5475 (mpp) REVERT: E 478 ASN cc_start: 0.8491 (m-40) cc_final: 0.8190 (m110) outliers start: 40 outliers final: 37 residues processed: 160 average time/residue: 0.1882 time to fit residues: 43.0097 Evaluate side-chains 171 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.131040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.103518 restraints weight = 10257.354| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.79 r_work: 0.2893 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8999 Z= 0.193 Angle : 0.558 9.953 12196 Z= 0.278 Chirality : 0.041 0.137 1388 Planarity : 0.003 0.042 1537 Dihedral : 5.260 83.959 1223 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.40 % Allowed : 26.42 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.25), residues: 1144 helix: 0.50 (0.33), residues: 270 sheet: -0.74 (0.28), residues: 346 loop : -2.29 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 474 HIS 0.006 0.001 HIS C 226 PHE 0.013 0.001 PHE E 431 TYR 0.016 0.001 TYR E 332 ARG 0.004 0.000 ARG F 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.08 seconds wall clock time: 39 minutes 54.66 seconds (2394.66 seconds total)