Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:06:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/04_2023/7jyi_22526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/04_2023/7jyi_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_22526/04_2023/7jyi_22526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/04_2023/7jyi_22526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/04_2023/7jyi_22526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jyi_22526/04_2023/7jyi_22526.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.53, per 1000 atoms: 0.63 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: 3.64 Conformation dependent library (CDL) restraints added in 1.6 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: 0.68 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: 2.95 Time building geometry restraints manager: 3.94 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: 3.600 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: 6.970 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.340 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.036 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 274 average time/residue: 0.2292 time to fit residues: 84.1659 Evaluate side-chains 184 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0836 time to fit residues: 4.8981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN C 219 HIS 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8999 Z= 0.170 Angle : 0.570 8.840 12196 Z= 0.291 Chirality : 0.042 0.158 1388 Planarity : 0.004 0.037 1537 Dihedral : 5.262 70.765 1219 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 3.67 % 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: -3.51 (0.22), residues: 1144 helix: -0.44 (0.32), residues: 256 sheet: -2.04 (0.25), residues: 362 loop : -3.55 (0.22), residues: 526 *********************** 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 218 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 204 average time/residue: 0.2156 time to fit residues: 60.5544 Evaluate side-chains 177 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1261 time to fit residues: 5.4608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 0.0970 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN ** E 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 8999 Z= 0.346 Angle : 0.636 9.361 12196 Z= 0.322 Chirality : 0.043 0.140 1388 Planarity : 0.004 0.041 1537 Dihedral : 5.390 81.308 1219 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.18 % Favored : 90.65 % Rotamer Outliers : 3.04 % 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: -3.13 (0.23), residues: 1144 helix: -0.21 (0.32), residues: 258 sheet: -1.77 (0.25), residues: 376 loop : -3.34 (0.23), residues: 510 *********************** 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 195 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 185 average time/residue: 0.2285 time to fit residues: 58.0727 Evaluate side-chains 164 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0876 time to fit residues: 4.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN E 447 GLN E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8999 Z= 0.157 Angle : 0.545 9.071 12196 Z= 0.277 Chirality : 0.040 0.146 1388 Planarity : 0.004 0.041 1537 Dihedral : 4.869 73.606 1219 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 1.57 % 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: -2.66 (0.23), residues: 1144 helix: 0.19 (0.33), residues: 262 sheet: -1.47 (0.27), residues: 348 loop : -3.04 (0.23), residues: 534 *********************** 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 168 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 163 average time/residue: 0.2097 time to fit residues: 48.2561 Evaluate side-chains 150 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1240 time to fit residues: 3.1367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 HIS C 172 ASN E 439 ASN E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.054 8999 Z= 0.497 Angle : 0.714 11.831 12196 Z= 0.358 Chirality : 0.047 0.144 1388 Planarity : 0.004 0.043 1537 Dihedral : 5.611 88.725 1219 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.62 % Favored : 90.21 % Rotamer Outliers : 3.14 % 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: -2.73 (0.23), residues: 1144 helix: -0.18 (0.32), residues: 270 sheet: -1.51 (0.26), residues: 386 loop : -3.01 (0.24), residues: 488 *********************** 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 177 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 165 average time/residue: 0.2069 time to fit residues: 48.4532 Evaluate side-chains 163 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0867 time to fit residues: 4.9595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN E 478 ASN ** 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: 0.8168 moved from start: 0.3507 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= 0.208 Angle : 0.582 9.632 12196 Z= 0.291 Chirality : 0.041 0.138 1388 Planarity : 0.004 0.041 1537 Dihedral : 5.194 86.644 1219 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 1.26 % 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: -2.37 (0.24), residues: 1144 helix: 0.08 (0.32), residues: 270 sheet: -1.21 (0.27), residues: 356 loop : -2.76 (0.25), residues: 518 *********************** 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 165 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 159 average time/residue: 0.2091 time to fit residues: 47.1665 Evaluate side-chains 152 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0808 time to fit residues: 2.4383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8999 Z= 0.178 Angle : 0.563 9.905 12196 Z= 0.281 Chirality : 0.041 0.135 1388 Planarity : 0.003 0.042 1537 Dihedral : 4.927 82.643 1219 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.78 % Favored : 92.05 % Rotamer Outliers : 1.15 % 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: -2.04 (0.24), residues: 1144 helix: 0.27 (0.33), residues: 272 sheet: -0.96 (0.27), residues: 352 loop : -2.56 (0.25), residues: 520 *********************** 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 154 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 148 average time/residue: 0.2190 time to fit residues: 45.2240 Evaluate side-chains 149 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0949 time to fit residues: 2.5457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8154 moved from start: 0.3744 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= 0.220 Angle : 0.584 11.100 12196 Z= 0.289 Chirality : 0.041 0.138 1388 Planarity : 0.004 0.042 1537 Dihedral : 4.946 82.903 1219 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 0.52 % 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: -1.94 (0.24), residues: 1144 helix: 0.34 (0.33), residues: 272 sheet: -0.85 (0.27), residues: 356 loop : -2.53 (0.25), residues: 516 *********************** 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 151 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 148 average time/residue: 0.2168 time to fit residues: 44.5606 Evaluate side-chains 144 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0952 time to fit residues: 2.0240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 8999 Z= 0.342 Angle : 0.651 10.347 12196 Z= 0.322 Chirality : 0.044 0.140 1388 Planarity : 0.004 0.043 1537 Dihedral : 5.270 89.281 1219 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.74 % Favored : 91.08 % Rotamer Outliers : 0.63 % 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: -1.96 (0.25), residues: 1144 helix: 0.26 (0.32), residues: 274 sheet: -0.88 (0.27), residues: 382 loop : -2.58 (0.26), residues: 488 *********************** 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 148 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 146 average time/residue: 0.2172 time to fit residues: 44.5672 Evaluate side-chains 145 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1081 time to fit residues: 2.0591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.3890 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= 0.212 Angle : 0.588 9.832 12196 Z= 0.293 Chirality : 0.041 0.137 1388 Planarity : 0.003 0.041 1537 Dihedral : 5.030 87.129 1219 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.10 % 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: 0.43 (0.33), residues: 272 sheet: -0.76 (0.28), residues: 346 loop : -2.41 (0.25), residues: 526 ********************** 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 144 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.2244 time to fit residues: 45.0358 Evaluate side-chains 137 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.101533 restraints weight = 10277.569| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.90 r_work: 0.2853 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3907 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= 0.245 Angle : 0.602 9.309 12196 Z= 0.299 Chirality : 0.042 0.136 1388 Planarity : 0.004 0.042 1537 Dihedral : 5.060 86.951 1219 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.43 % Rotamer Outliers : 0.21 % 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: -1.77 (0.25), residues: 1144 helix: 0.46 (0.33), residues: 272 sheet: -0.64 (0.29), residues: 328 loop : -2.44 (0.25), residues: 544 =============================================================================== Job complete usr+sys time: 2050.48 seconds wall clock time: 38 minutes 7.37 seconds (2287.37 seconds total)