Starting phenix.real_space_refine on Wed Feb 14 20:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuv_29481/02_2024/8fuv_29481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuv_29481/02_2024/8fuv_29481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuv_29481/02_2024/8fuv_29481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuv_29481/02_2024/8fuv_29481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuv_29481/02_2024/8fuv_29481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuv_29481/02_2024/8fuv_29481.pdb" } resolution = 3.1 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= 0.001 sd= 0.006 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 36 5.16 5 C 6394 2.51 5 N 1755 2.21 5 O 1985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 192": "OD1" <-> "OD2" Residue "F ASP 216": "OD1" <-> "OD2" Residue "F ASP 332": "OD1" <-> "OD2" Residue "F PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 492": "OD1" <-> "OD2" Residue "T PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 21": "OE1" <-> "OE2" Residue "T ASP 25": "OD1" <-> "OD2" Residue "T ASP 30": "OD1" <-> "OD2" Residue "T PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 38": "OD1" <-> "OD2" Residue "T ASP 46": "OD1" <-> "OD2" Residue "T GLU 67": "OE1" <-> "OE2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10170 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3780 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain: "T" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Time building chain proxies: 6.05, per 1000 atoms: 0.59 Number of scatterers: 10170 At special positions: 0 Unit cell: (162.4, 129.92, 82.88, 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 36 16.00 O 1985 8.00 N 1755 7.00 C 6394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 30 sheets defined 21.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'F' and resid 46 through 55 removed outlier: 3.554A pdb=" N VAL F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.511A pdb=" N GLN F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 150 Processing helix chain 'F' and resid 153 through 158 removed outlier: 4.304A pdb=" N GLN F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 removed outlier: 3.613A pdb=" N ALA F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.542A pdb=" N ALA F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 254 Processing helix chain 'F' and resid 265 through 276 removed outlier: 4.244A pdb=" N GLY F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU F 275 " --> pdb=" O THR F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.594A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 342 removed outlier: 3.753A pdb=" N SER F 342 " --> pdb=" O THR F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 398 Processing helix chain 'F' and resid 405 through 427 Proline residue: F 418 - end of helix Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 451 through 459 removed outlier: 3.785A pdb=" N GLN F 455 " --> pdb=" O ARG F 451 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 45 No H-bonds generated for 'chain 'T' and resid 43 through 45' Processing helix chain 'T' and resid 66 through 80 removed outlier: 3.707A pdb=" N ASN T 79 " --> pdb=" O LEU T 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 66 through 80 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 66 through 80 Processing sheet with id=AA1, first strand: chain 'F' and resid 42 through 44 removed outlier: 6.408A pdb=" N ARG F 28 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 160 through 163 removed outlier: 3.591A pdb=" N THR F 171 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 172 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'F' and resid 260 through 264 removed outlier: 6.492A pdb=" N TYR F 260 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN F 285 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL F 262 " --> pdb=" O ASN F 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352 Processing sheet with id=AA6, first strand: chain 'F' and resid 461 through 471 Processing sheet with id=AA7, first strand: chain 'T' and resid 17 through 19 removed outlier: 6.476A pdb=" N VAL T 92 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN T 108 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG T 134 " --> pdb=" O THR T 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU T 56 " --> pdb=" O PHE T 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 17 through 19 removed outlier: 6.476A pdb=" N VAL T 92 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN T 108 " --> pdb=" O VAL T 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'T' and resid 37 through 41 Processing sheet with id=AB2, first strand: chain 'T' and resid 113 through 114 Processing sheet with id=AB3, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.431A pdb=" N VAL A 92 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN A 108 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.431A pdb=" N VAL A 92 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN A 108 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AB6, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 17 through 19 removed outlier: 6.461A pdb=" N VAL B 92 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN B 108 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 134 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 17 through 19 removed outlier: 6.461A pdb=" N VAL B 92 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN B 108 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AC2, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.403A pdb=" N VAL C 92 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN C 108 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.403A pdb=" N VAL C 92 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN C 108 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AC7, first strand: chain 'D' and resid 17 through 19 removed outlier: 6.373A pdb=" N VAL D 92 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN D 108 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 134 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 17 through 19 removed outlier: 6.373A pdb=" N VAL D 92 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN D 108 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 37 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 17 through 19 removed outlier: 6.382A pdb=" N VAL E 92 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN E 108 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 134 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 17 through 19 removed outlier: 6.382A pdb=" N VAL E 92 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN E 108 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 37 through 41 454 hydrogen bonds defined for protein. 1236 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: 3.26 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3443 1.34 - 1.46: 2019 1.46 - 1.58: 4826 1.58 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 10347 Sorted by residual: bond pdb=" CA ASP D 84 " pdb=" CB ASP D 84 " ideal model delta sigma weight residual 1.524 1.576 -0.052 1.62e-02 3.81e+03 1.03e+01 bond pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CA GLN F 417 " pdb=" C GLN F 417 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 9.19e-01 bond pdb=" N PRO F 101 " pdb=" CA PRO F 101 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 8.84e-01 bond pdb=" CG1 ILE T 112 " pdb=" CD1 ILE T 112 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.42e-01 ... (remaining 10342 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 313 107.29 - 113.95: 5920 113.95 - 120.62: 3866 120.62 - 127.28: 3913 127.28 - 133.95: 85 Bond angle restraints: 14097 Sorted by residual: angle pdb=" C ASN F 293 " pdb=" N ASP F 294 " pdb=" CA ASP F 294 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 angle pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " pdb=" CD LYS B 83 " ideal model delta sigma weight residual 111.30 118.26 -6.96 2.30e+00 1.89e-01 9.16e+00 angle pdb=" CA LYS B 83 " pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 angle pdb=" C GLY F 13 " pdb=" N VAL F 14 " pdb=" CA VAL F 14 " ideal model delta sigma weight residual 122.97 120.41 2.56 9.80e-01 1.04e+00 6.84e+00 angle pdb=" CG1 ILE T 29 " pdb=" CB ILE T 29 " pdb=" CG2 ILE T 29 " ideal model delta sigma weight residual 110.70 103.53 7.17 3.00e+00 1.11e-01 5.71e+00 ... (remaining 14092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 5532 15.22 - 30.43: 481 30.43 - 45.65: 121 45.65 - 60.86: 20 60.86 - 76.08: 11 Dihedral angle restraints: 6165 sinusoidal: 2282 harmonic: 3883 Sorted by residual: dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N ALA B 24 " pdb=" CA ALA B 24 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE E 23 " pdb=" C PHE E 23 " pdb=" N ALA E 24 " pdb=" CA ALA E 24 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE T 23 " pdb=" C PHE T 23 " pdb=" N ALA T 24 " pdb=" CA ALA T 24 " ideal model delta harmonic sigma weight residual -180.00 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 6162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1197 0.042 - 0.083: 312 0.083 - 0.125: 136 0.125 - 0.166: 16 0.166 - 0.208: 3 Chirality restraints: 1664 Sorted by residual: chirality pdb=" CB ILE T 29 " pdb=" CA ILE T 29 " pdb=" CG1 ILE T 29 " pdb=" CG2 ILE T 29 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 29 " pdb=" CA ILE A 29 " pdb=" CG1 ILE A 29 " pdb=" CG2 ILE A 29 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 1661 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 63 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 64 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 63 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO D 64 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 63 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 64 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.024 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 379 2.72 - 3.26: 9612 3.26 - 3.81: 15117 3.81 - 4.35: 18531 4.35 - 4.90: 32730 Nonbonded interactions: 76369 Sorted by model distance: nonbonded pdb=" OD2 ASP F 192 " pdb=" OG SER F 194 " model vdw 2.169 2.440 nonbonded pdb=" OG SER F 72 " pdb=" O SER F 74 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR F 162 " pdb=" OG1 THR F 171 " model vdw 2.296 2.440 nonbonded pdb=" O ASN F 255 " pdb=" NZ LYS F 385 " model vdw 2.306 2.520 nonbonded pdb=" OD1 ASN F 285 " pdb=" OH TYR F 360 " model vdw 2.358 2.440 ... (remaining 76364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'T' } 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: 2.110 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: 6.070 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.060 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.003 0.052 10347 Z= 0.208 Angle : 0.590 7.171 14097 Z= 0.337 Chirality : 0.045 0.208 1664 Planarity : 0.004 0.044 1857 Dihedral : 12.825 76.078 3667 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.17 (0.22), residues: 1354 helix: 3.23 (0.34), residues: 236 sheet: 0.46 (0.26), residues: 403 loop : -1.72 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 462 PHE 0.012 0.001 PHE E 34 TYR 0.010 0.001 TYR F 67 ARG 0.003 0.000 ARG T 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.083 Fit side-chains REVERT: F 137 MET cc_start: 0.7539 (pmm) cc_final: 0.7195 (pmm) REVERT: F 490 LYS cc_start: 0.5579 (mptt) cc_final: 0.5189 (mmtt) REVERT: E 23 PHE cc_start: 0.5933 (t80) cc_final: 0.5695 (t80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2824 time to fit residues: 59.1624 Evaluate side-chains 149 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.0040 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10347 Z= 0.183 Angle : 0.518 5.729 14097 Z= 0.287 Chirality : 0.044 0.141 1664 Planarity : 0.004 0.043 1857 Dihedral : 4.421 20.210 1447 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.65 % Allowed : 6.55 % Favored : 92.80 % 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: -0.29 (0.23), residues: 1354 helix: 2.69 (0.33), residues: 253 sheet: 0.28 (0.25), residues: 465 loop : -1.85 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 250 PHE 0.013 0.002 PHE A 34 TYR 0.011 0.001 TYR F 67 ARG 0.003 0.000 ARG T 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.242 Fit side-chains REVERT: F 137 MET cc_start: 0.7537 (pmm) cc_final: 0.7223 (pmm) REVERT: E 23 PHE cc_start: 0.5973 (t80) cc_final: 0.5766 (t80) outliers start: 7 outliers final: 5 residues processed: 157 average time/residue: 0.2978 time to fit residues: 61.4571 Evaluate side-chains 151 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.4980 chunk 37 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10347 Z= 0.248 Angle : 0.530 5.080 14097 Z= 0.297 Chirality : 0.045 0.153 1664 Planarity : 0.005 0.049 1857 Dihedral : 4.694 26.085 1447 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.48 % Allowed : 9.04 % Favored : 89.48 % 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: -0.38 (0.22), residues: 1354 helix: 2.69 (0.34), residues: 253 sheet: 0.06 (0.24), residues: 475 loop : -1.82 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 462 PHE 0.016 0.002 PHE B 23 TYR 0.012 0.001 TYR F 67 ARG 0.003 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.146 Fit side-chains REVERT: F 118 MET cc_start: 0.6402 (tmm) cc_final: 0.6139 (tmm) REVERT: F 137 MET cc_start: 0.7544 (pmm) cc_final: 0.7260 (pmm) REVERT: F 490 LYS cc_start: 0.5906 (mptt) cc_final: 0.5699 (mptt) REVERT: E 23 PHE cc_start: 0.5983 (t80) cc_final: 0.5762 (t80) outliers start: 16 outliers final: 5 residues processed: 159 average time/residue: 0.2801 time to fit residues: 58.8498 Evaluate side-chains 147 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10347 Z= 0.334 Angle : 0.573 5.391 14097 Z= 0.322 Chirality : 0.047 0.178 1664 Planarity : 0.005 0.053 1857 Dihedral : 5.027 28.724 1447 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.75 % Allowed : 10.61 % Favored : 87.64 % 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: -0.51 (0.22), residues: 1354 helix: 2.56 (0.34), residues: 253 sheet: -0.01 (0.24), residues: 465 loop : -1.87 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 462 PHE 0.020 0.002 PHE C 23 TYR 0.013 0.002 TYR F 67 ARG 0.004 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.227 Fit side-chains REVERT: F 137 MET cc_start: 0.7606 (pmm) cc_final: 0.7366 (pmm) REVERT: F 490 LYS cc_start: 0.5939 (mptt) cc_final: 0.5630 (mptt) REVERT: T 69 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7734 (tm-30) REVERT: E 23 PHE cc_start: 0.6091 (t80) cc_final: 0.5856 (t80) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.2781 time to fit residues: 58.9480 Evaluate side-chains 154 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 3.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10347 Z= 0.210 Angle : 0.518 4.820 14097 Z= 0.290 Chirality : 0.045 0.148 1664 Planarity : 0.005 0.050 1857 Dihedral : 4.852 28.746 1447 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.57 % Allowed : 12.55 % Favored : 85.89 % 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: -0.49 (0.22), residues: 1354 helix: 2.64 (0.33), residues: 253 sheet: -0.11 (0.24), residues: 475 loop : -1.82 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 462 PHE 0.012 0.002 PHE A 23 TYR 0.011 0.001 TYR F 67 ARG 0.003 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.222 Fit side-chains REVERT: F 118 MET cc_start: 0.6512 (tmm) cc_final: 0.6275 (tmm) REVERT: F 137 MET cc_start: 0.7693 (pmm) cc_final: 0.7412 (pmm) REVERT: F 490 LYS cc_start: 0.5895 (mptt) cc_final: 0.5581 (mptt) REVERT: D 23 PHE cc_start: 0.6386 (t80) cc_final: 0.6143 (t80) REVERT: E 23 PHE cc_start: 0.6017 (t80) cc_final: 0.5750 (t80) outliers start: 17 outliers final: 12 residues processed: 156 average time/residue: 0.2735 time to fit residues: 56.8507 Evaluate side-chains 153 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 21 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 10 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 0.1980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10347 Z= 0.182 Angle : 0.495 4.772 14097 Z= 0.275 Chirality : 0.044 0.141 1664 Planarity : 0.004 0.049 1857 Dihedral : 4.645 27.402 1447 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.98 % Favored : 93.80 % Rotamer: Outliers : 2.03 % Allowed : 12.64 % Favored : 85.33 % 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: -0.47 (0.22), residues: 1354 helix: 2.76 (0.33), residues: 253 sheet: -0.13 (0.24), residues: 475 loop : -1.81 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 462 PHE 0.013 0.001 PHE A 23 TYR 0.011 0.001 TYR F 67 ARG 0.003 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.190 Fit side-chains REVERT: F 137 MET cc_start: 0.7657 (pmm) cc_final: 0.7380 (pmm) REVERT: F 490 LYS cc_start: 0.5917 (mptt) cc_final: 0.5594 (mptt) REVERT: D 23 PHE cc_start: 0.6310 (t80) cc_final: 0.6104 (t80) REVERT: E 23 PHE cc_start: 0.6025 (t80) cc_final: 0.5765 (t80) outliers start: 22 outliers final: 16 residues processed: 162 average time/residue: 0.2743 time to fit residues: 59.3917 Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 21 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 129 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10347 Z= 0.307 Angle : 0.565 7.382 14097 Z= 0.316 Chirality : 0.046 0.170 1664 Planarity : 0.005 0.053 1857 Dihedral : 5.047 30.028 1447 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.61 % Favored : 93.94 % Rotamer: Outliers : 2.58 % Allowed : 12.36 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1354 helix: 2.65 (0.34), residues: 253 sheet: -0.16 (0.24), residues: 475 loop : -1.82 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 199 PHE 0.016 0.002 PHE E 34 TYR 0.012 0.002 TYR F 67 ARG 0.004 0.000 ARG T 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.155 Fit side-chains REVERT: F 137 MET cc_start: 0.7697 (pmm) cc_final: 0.7443 (pmm) REVERT: F 490 LYS cc_start: 0.5940 (mptt) cc_final: 0.5614 (mptt) REVERT: T 69 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7728 (tm-30) REVERT: E 23 PHE cc_start: 0.6138 (t80) cc_final: 0.5895 (t80) outliers start: 28 outliers final: 20 residues processed: 169 average time/residue: 0.2614 time to fit residues: 59.2609 Evaluate side-chains 164 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 21 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 101 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10347 Z= 0.306 Angle : 0.567 7.432 14097 Z= 0.317 Chirality : 0.046 0.168 1664 Planarity : 0.005 0.053 1857 Dihedral : 5.109 28.925 1447 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 2.31 % Allowed : 12.73 % Favored : 84.96 % 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: -0.56 (0.22), residues: 1354 helix: 2.53 (0.33), residues: 253 sheet: -0.20 (0.24), residues: 481 loop : -1.80 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 199 PHE 0.015 0.002 PHE E 34 TYR 0.012 0.002 TYR F 67 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.212 Fit side-chains REVERT: F 137 MET cc_start: 0.7678 (pmm) cc_final: 0.7438 (pmm) REVERT: F 490 LYS cc_start: 0.5921 (mptt) cc_final: 0.5594 (mptt) REVERT: T 8 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9007 (p) REVERT: T 69 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 23 PHE cc_start: 0.6137 (t80) cc_final: 0.5877 (t80) outliers start: 25 outliers final: 21 residues processed: 168 average time/residue: 0.2651 time to fit residues: 59.7717 Evaluate side-chains 166 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10347 Z= 0.272 Angle : 0.560 7.766 14097 Z= 0.313 Chirality : 0.046 0.159 1664 Planarity : 0.005 0.052 1857 Dihedral : 5.031 29.649 1447 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.76 % Favored : 93.80 % Rotamer: Outliers : 2.77 % Allowed : 12.36 % Favored : 84.87 % 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: -0.59 (0.22), residues: 1354 helix: 2.57 (0.34), residues: 253 sheet: -0.25 (0.24), residues: 475 loop : -1.81 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 199 PHE 0.014 0.002 PHE E 34 TYR 0.012 0.001 TYR F 67 ARG 0.003 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.060 Fit side-chains REVERT: F 137 MET cc_start: 0.7697 (pmm) cc_final: 0.7454 (pmm) REVERT: T 8 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9011 (p) REVERT: E 23 PHE cc_start: 0.6136 (t80) cc_final: 0.5886 (t80) outliers start: 30 outliers final: 23 residues processed: 171 average time/residue: 0.2636 time to fit residues: 59.9434 Evaluate side-chains 168 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10347 Z= 0.309 Angle : 0.581 7.848 14097 Z= 0.326 Chirality : 0.047 0.248 1664 Planarity : 0.006 0.068 1857 Dihedral : 5.126 30.763 1447 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.87 % Rotamer: Outliers : 2.49 % Allowed : 13.10 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1354 helix: 2.47 (0.34), residues: 253 sheet: -0.25 (0.24), residues: 481 loop : -1.81 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 199 PHE 0.015 0.002 PHE B 34 TYR 0.012 0.002 TYR F 67 ARG 0.011 0.001 ARG F 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.200 Fit side-chains REVERT: F 137 MET cc_start: 0.7677 (pmm) cc_final: 0.7424 (pmm) REVERT: T 8 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9009 (p) REVERT: T 69 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 23 PHE cc_start: 0.6163 (t80) cc_final: 0.5905 (t80) outliers start: 27 outliers final: 24 residues processed: 169 average time/residue: 0.2847 time to fit residues: 64.5379 Evaluate side-chains 168 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071192 restraints weight = 23121.615| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.58 r_work: 0.2901 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10347 Z= 0.260 Angle : 0.556 7.753 14097 Z= 0.311 Chirality : 0.046 0.219 1664 Planarity : 0.005 0.052 1857 Dihedral : 4.984 29.631 1447 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.76 % Favored : 93.80 % Rotamer: Outliers : 2.31 % Allowed : 13.10 % Favored : 84.59 % 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: -0.61 (0.22), residues: 1354 helix: 2.54 (0.34), residues: 253 sheet: -0.26 (0.24), residues: 475 loop : -1.81 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 199 PHE 0.014 0.002 PHE B 34 TYR 0.012 0.001 TYR F 67 ARG 0.006 0.000 ARG F 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.75 seconds wall clock time: 41 minutes 24.43 seconds (2484.43 seconds total)