Starting phenix.real_space_refine on Sun Apr 7 18:03:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/04_2024/8j7x_36052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/04_2024/8j7x_36052.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/8j7x_36052/04_2024/8j7x_36052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/04_2024/8j7x_36052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/04_2024/8j7x_36052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/04_2024/8j7x_36052.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 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 48 5.16 5 C 7122 2.51 5 N 1860 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2258 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 2 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2258 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 2 Time building chain proxies: 5.77, per 1000 atoms: 0.52 Number of scatterers: 11136 At special positions: 0 Unit cell: (79.06, 116.82, 162.84, 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 48 16.00 O 2106 8.00 N 1860 7.00 C 7122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " 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: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 33.8% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.253A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Processing helix chain 'A' and resid 60 through 88 removed outlier: 4.436A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 Processing helix chain 'A' and resid 138 through 159 Processing helix chain 'A' and resid 231 through 260 removed outlier: 3.522A pdb=" N GLN A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.321A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.873A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.713A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.661A pdb=" N TYR E 32 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.955A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.660A pdb=" N TYR F 32 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.955A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.873A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.713A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 60 through 88 removed outlier: 4.436A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 131 Processing helix chain 'B' and resid 138 through 159 Processing helix chain 'B' and resid 231 through 260 removed outlier: 3.521A pdb=" N GLN B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.321A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 5.692A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 334 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N TYR A 368 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 336 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN A 370 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 338 " --> pdb=" O GLN A 370 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 340 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.719A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.804A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.768A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.732A pdb=" N ILE C 209 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.720A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.804A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.767A pdb=" N ASN D 141 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.732A pdb=" N ILE D 209 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 330 removed outlier: 5.691A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR B 334 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N TYR B 368 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY B 336 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN B 370 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 338 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP B 372 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 340 " --> pdb=" O ASP B 372 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1818 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: 4.25 Time building geometry restraints manager: 4.50 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: 3553 1.34 - 1.46: 2703 1.46 - 1.58: 5078 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 11404 Sorted by residual: bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.66e-01 bond pdb=" CG PRO D 145 " pdb=" CD PRO D 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.50e-01 bond pdb=" CG PRO D 99 " pdb=" CD PRO D 99 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.45e-01 bond pdb=" CG PRO C 145 " pdb=" CD PRO C 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.22e-01 bond pdb=" CG PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.54e-01 ... (remaining 11399 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 362 107.13 - 113.84: 6466 113.84 - 120.55: 4272 120.55 - 127.26: 4290 127.26 - 133.97: 136 Bond angle restraints: 15526 Sorted by residual: angle pdb=" C ARG C 54 " pdb=" N ALA C 55 " pdb=" CA ALA C 55 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.91e+00 angle pdb=" C ARG D 54 " pdb=" N ALA D 55 " pdb=" CA ALA D 55 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.74e+00 angle pdb=" N ALA C 55 " pdb=" CA ALA C 55 " pdb=" C ALA C 55 " ideal model delta sigma weight residual 110.80 114.36 -3.56 2.13e+00 2.20e-01 2.79e+00 angle pdb=" N ASP A 94 " pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " ideal model delta sigma weight residual 113.65 111.21 2.44 1.47e+00 4.63e-01 2.75e+00 angle pdb=" N ALA D 55 " pdb=" CA ALA D 55 " pdb=" C ALA D 55 " ideal model delta sigma weight residual 110.80 114.33 -3.53 2.13e+00 2.20e-01 2.74e+00 ... (remaining 15521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6414 17.98 - 35.96: 280 35.96 - 53.94: 40 53.94 - 71.92: 8 71.92 - 89.90: 2 Dihedral angle restraints: 6744 sinusoidal: 2566 harmonic: 4178 Sorted by residual: dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 121.69 -28.69 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 121.68 -28.68 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CA ARG B 296 " pdb=" CB ARG B 296 " pdb=" CG ARG B 296 " pdb=" CD ARG B 296 " ideal model delta sinusoidal sigma weight residual -180.00 -125.76 -54.24 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 6741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1069 0.028 - 0.055: 450 0.055 - 0.083: 122 0.083 - 0.110: 104 0.110 - 0.138: 35 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE D 52 " pdb=" N ILE D 52 " pdb=" C ILE D 52 " pdb=" CB ILE D 52 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1777 not shown) Planarity restraints: 1966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO F 189 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 188 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO E 189 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 189 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 189 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E 193 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO E 194 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO E 194 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 194 " -0.013 5.00e-02 4.00e+02 ... (remaining 1963 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1070 2.75 - 3.29: 10728 3.29 - 3.83: 18446 3.83 - 4.36: 21401 4.36 - 4.90: 38584 Nonbonded interactions: 90229 Sorted by model distance: nonbonded pdb=" OG SER C 125 " pdb=" O PRO E 128 " model vdw 2.213 2.440 nonbonded pdb=" O PRO F 128 " pdb=" OG SER D 125 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU D 189 " pdb=" NH2 ARG D 192 " model vdw 2.288 2.520 nonbonded pdb=" OE1 GLU C 189 " pdb=" NH2 ARG C 192 " model vdw 2.289 2.520 nonbonded pdb=" O THR F 192 " pdb=" N GLU F 196 " model vdw 2.302 2.520 ... (remaining 90224 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 5.530 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.190 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.002 0.035 11404 Z= 0.149 Angle : 0.448 5.371 15526 Z= 0.236 Chirality : 0.040 0.138 1780 Planarity : 0.003 0.041 1966 Dihedral : 10.166 89.901 4024 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.39 % Favored : 97.46 % Rotamer: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.75 (0.23), residues: 1420 helix: 3.14 (0.24), residues: 430 sheet: 0.85 (0.25), residues: 462 loop : -0.21 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 108 HIS 0.003 0.001 HIS B 70 PHE 0.015 0.001 PHE A 123 TYR 0.010 0.001 TYR E 94 ARG 0.003 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.7857 (mm) cc_final: 0.7604 (mm) REVERT: A 257 MET cc_start: 0.6632 (mmt) cc_final: 0.6334 (mmt) REVERT: A 345 ASP cc_start: 0.6759 (p0) cc_final: 0.6453 (p0) outliers start: 2 outliers final: 0 residues processed: 346 average time/residue: 0.2320 time to fit residues: 112.7539 Evaluate side-chains 213 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 HIS ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 361 GLN C 6 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 214 ASN E 86 GLN E 160 ASN F 16 GLN D 6 GLN D 128 GLN D 142 ASN D 161 ASN B 137 HIS B 232 GLN B 354 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11404 Z= 0.249 Angle : 0.573 8.444 15526 Z= 0.297 Chirality : 0.043 0.164 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.851 15.320 1538 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.03 % Favored : 96.83 % Rotamer: Outliers : 3.06 % Allowed : 9.42 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.52 (0.23), residues: 1420 helix: 2.77 (0.24), residues: 434 sheet: 0.90 (0.25), residues: 462 loop : -0.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 167 HIS 0.004 0.001 HIS A 70 PHE 0.038 0.002 PHE A 73 TYR 0.027 0.001 TYR A 319 ARG 0.004 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7888 (tptt) cc_final: 0.7622 (tppt) REVERT: A 257 MET cc_start: 0.6585 (mmt) cc_final: 0.6269 (mmt) REVERT: F 1 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6352 (tm-30) REVERT: B 33 LYS cc_start: 0.7533 (tptp) cc_final: 0.7144 (tppt) REVERT: B 120 PHE cc_start: 0.7354 (t80) cc_final: 0.7107 (t80) REVERT: B 294 MET cc_start: 0.8011 (mmm) cc_final: 0.7789 (mmt) outliers start: 38 outliers final: 21 residues processed: 237 average time/residue: 0.2212 time to fit residues: 75.8818 Evaluate side-chains 211 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 361 GLN C 96 ASN C 214 ASN E 73 ASN E 77 GLN F 160 ASN B 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11404 Z= 0.282 Angle : 0.571 10.743 15526 Z= 0.295 Chirality : 0.043 0.148 1780 Planarity : 0.004 0.045 1966 Dihedral : 3.949 14.947 1538 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.96 % Favored : 96.90 % Rotamer: Outliers : 3.22 % Allowed : 12.08 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1420 helix: 2.76 (0.23), residues: 432 sheet: 0.82 (0.25), residues: 460 loop : -0.38 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 159 HIS 0.020 0.001 HIS B 137 PHE 0.026 0.002 PHE A 73 TYR 0.018 0.001 TYR E 32 ARG 0.006 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 1.327 Fit side-chains REVERT: A 33 LYS cc_start: 0.7816 (tptt) cc_final: 0.7553 (tppt) REVERT: A 257 MET cc_start: 0.6578 (mmt) cc_final: 0.6330 (mmt) REVERT: A 288 GLU cc_start: 0.6739 (tt0) cc_final: 0.6510 (tt0) REVERT: C 158 GLU cc_start: 0.7918 (tp30) cc_final: 0.7356 (tp30) REVERT: C 179 MET cc_start: 0.7081 (tpt) cc_final: 0.6725 (tpt) REVERT: E 32 TYR cc_start: 0.7966 (m-80) cc_final: 0.7605 (m-80) REVERT: F 1 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6585 (tm-30) REVERT: F 178 ASP cc_start: 0.7298 (t70) cc_final: 0.7026 (t70) REVERT: B 143 LEU cc_start: 0.8269 (pp) cc_final: 0.7972 (tt) outliers start: 40 outliers final: 30 residues processed: 224 average time/residue: 0.2256 time to fit residues: 72.9347 Evaluate side-chains 220 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.0470 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN C 214 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN B 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11404 Z= 0.242 Angle : 0.556 9.699 15526 Z= 0.282 Chirality : 0.042 0.158 1780 Planarity : 0.004 0.041 1966 Dihedral : 3.884 15.415 1538 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.38 % Allowed : 13.69 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.52 (0.23), residues: 1420 helix: 2.87 (0.23), residues: 432 sheet: 0.83 (0.24), residues: 460 loop : -0.40 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 167 HIS 0.006 0.001 HIS A 70 PHE 0.025 0.002 PHE B 123 TYR 0.016 0.001 TYR C 53 ARG 0.008 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7773 (tptt) cc_final: 0.7472 (tppt) REVERT: A 257 MET cc_start: 0.6636 (mmt) cc_final: 0.6316 (mmt) REVERT: A 345 ASP cc_start: 0.7765 (p0) cc_final: 0.7463 (p0) REVERT: C 158 GLU cc_start: 0.7936 (tp30) cc_final: 0.7450 (tp30) REVERT: C 179 MET cc_start: 0.7287 (tpt) cc_final: 0.7047 (tpt) REVERT: C 194 ASN cc_start: 0.7684 (t0) cc_final: 0.7341 (t0) REVERT: C 214 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6815 (t0) REVERT: F 178 ASP cc_start: 0.7254 (t70) cc_final: 0.7029 (t70) REVERT: D 154 ILE cc_start: 0.7428 (mm) cc_final: 0.7145 (mt) REVERT: D 179 MET cc_start: 0.6780 (ttt) cc_final: 0.6293 (ttt) REVERT: B 50 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: B 143 LEU cc_start: 0.8216 (pp) cc_final: 0.7997 (tt) outliers start: 42 outliers final: 28 residues processed: 220 average time/residue: 0.2178 time to fit residues: 69.6576 Evaluate side-chains 211 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.0010 chunk 115 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN B 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11404 Z= 0.216 Angle : 0.555 9.480 15526 Z= 0.281 Chirality : 0.042 0.194 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.866 16.419 1538 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.86 % Allowed : 13.12 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.57 (0.23), residues: 1420 helix: 2.94 (0.23), residues: 432 sheet: 0.87 (0.24), residues: 460 loop : -0.43 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 167 HIS 0.003 0.001 HIS B 138 PHE 0.026 0.001 PHE B 123 TYR 0.015 0.001 TYR C 53 ARG 0.012 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 1.350 Fit side-chains REVERT: A 33 LYS cc_start: 0.7771 (tptt) cc_final: 0.7478 (tppt) REVERT: A 257 MET cc_start: 0.6656 (mmt) cc_final: 0.6322 (mmt) REVERT: C 158 GLU cc_start: 0.7874 (tp30) cc_final: 0.7400 (tp30) REVERT: C 179 MET cc_start: 0.7365 (tpt) cc_final: 0.7054 (tpt) REVERT: F 6 GLU cc_start: 0.7772 (mp0) cc_final: 0.7466 (mp0) REVERT: D 154 ILE cc_start: 0.7469 (mm) cc_final: 0.7226 (mt) REVERT: B 33 LYS cc_start: 0.7544 (tptt) cc_final: 0.7133 (tppt) REVERT: B 50 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7306 (m-80) outliers start: 48 outliers final: 34 residues processed: 217 average time/residue: 0.2203 time to fit residues: 69.1843 Evaluate side-chains 218 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.0020 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN B 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11404 Z= 0.208 Angle : 0.578 13.190 15526 Z= 0.290 Chirality : 0.043 0.277 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.865 16.627 1538 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.38 % Allowed : 13.85 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.54 (0.23), residues: 1420 helix: 2.90 (0.23), residues: 432 sheet: 0.91 (0.25), residues: 460 loop : -0.47 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.002 0.001 HIS A 70 PHE 0.030 0.001 PHE B 120 TYR 0.015 0.001 TYR C 53 ARG 0.007 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.375 Fit side-chains REVERT: A 33 LYS cc_start: 0.7726 (tptt) cc_final: 0.7436 (tppt) REVERT: A 242 LEU cc_start: 0.8609 (tt) cc_final: 0.8303 (mt) REVERT: A 257 MET cc_start: 0.6581 (mmt) cc_final: 0.6237 (mmt) REVERT: C 158 GLU cc_start: 0.7843 (tp30) cc_final: 0.7371 (tp30) REVERT: C 179 MET cc_start: 0.7489 (tpt) cc_final: 0.7167 (tpt) REVERT: C 194 ASN cc_start: 0.8133 (t0) cc_final: 0.7107 (t0) REVERT: D 154 ILE cc_start: 0.7551 (mm) cc_final: 0.7290 (mt) REVERT: B 50 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7410 (m-80) outliers start: 42 outliers final: 34 residues processed: 214 average time/residue: 0.2128 time to fit residues: 66.9671 Evaluate side-chains 216 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN F 16 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11404 Z= 0.193 Angle : 0.590 15.117 15526 Z= 0.290 Chirality : 0.042 0.187 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.824 16.679 1538 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.62 % Allowed : 14.17 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.55 (0.23), residues: 1420 helix: 2.91 (0.23), residues: 432 sheet: 0.90 (0.24), residues: 460 loop : -0.48 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 167 HIS 0.007 0.001 HIS B 137 PHE 0.028 0.002 PHE B 117 TYR 0.014 0.001 TYR C 53 ARG 0.006 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.6555 (mmt) cc_final: 0.6196 (mmt) REVERT: C 158 GLU cc_start: 0.7765 (tp30) cc_final: 0.7274 (tp30) REVERT: C 179 MET cc_start: 0.7530 (tpt) cc_final: 0.7163 (tpt) REVERT: F 6 GLU cc_start: 0.7773 (mp0) cc_final: 0.7485 (mp0) REVERT: D 154 ILE cc_start: 0.7591 (mm) cc_final: 0.7371 (mt) REVERT: B 50 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7412 (m-80) outliers start: 45 outliers final: 35 residues processed: 217 average time/residue: 0.2037 time to fit residues: 65.2552 Evaluate side-chains 220 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN F 73 ASN B 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11404 Z= 0.185 Angle : 0.597 15.187 15526 Z= 0.294 Chirality : 0.043 0.242 1780 Planarity : 0.004 0.042 1966 Dihedral : 3.809 16.508 1538 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.06 % Allowed : 15.22 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.59 (0.23), residues: 1420 helix: 2.92 (0.23), residues: 432 sheet: 0.95 (0.24), residues: 466 loop : -0.45 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 167 HIS 0.013 0.001 HIS A 70 PHE 0.029 0.002 PHE A 149 TYR 0.014 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.6659 (mmt) cc_final: 0.6277 (mmt) REVERT: A 258 MET cc_start: 0.7033 (mmm) cc_final: 0.6542 (mmm) REVERT: C 158 GLU cc_start: 0.7721 (tp30) cc_final: 0.7252 (tp30) REVERT: C 179 MET cc_start: 0.7580 (tpt) cc_final: 0.7175 (tpt) REVERT: F 6 GLU cc_start: 0.7693 (mp0) cc_final: 0.7433 (mp0) REVERT: D 154 ILE cc_start: 0.7583 (mm) cc_final: 0.7357 (mt) REVERT: B 50 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7407 (m-80) outliers start: 38 outliers final: 30 residues processed: 205 average time/residue: 0.2035 time to fit residues: 61.3229 Evaluate side-chains 208 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 54 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 82 optimal weight: 0.0470 chunk 132 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11404 Z= 0.169 Angle : 0.602 15.555 15526 Z= 0.295 Chirality : 0.042 0.232 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.687 16.192 1538 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.22 % Allowed : 15.06 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.61 (0.23), residues: 1420 helix: 2.88 (0.23), residues: 432 sheet: 0.99 (0.24), residues: 466 loop : -0.43 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 167 HIS 0.003 0.001 HIS B 138 PHE 0.032 0.001 PHE B 123 TYR 0.014 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.7190 (mmm) cc_final: 0.6822 (mmm) REVERT: C 158 GLU cc_start: 0.7719 (tp30) cc_final: 0.7209 (tp30) REVERT: C 179 MET cc_start: 0.7555 (tpt) cc_final: 0.7179 (tpt) REVERT: E 178 ASP cc_start: 0.7696 (t70) cc_final: 0.7415 (t0) REVERT: D 154 ILE cc_start: 0.7589 (mm) cc_final: 0.7366 (mt) REVERT: B 50 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7380 (m-80) outliers start: 40 outliers final: 32 residues processed: 215 average time/residue: 0.2348 time to fit residues: 74.7604 Evaluate side-chains 218 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 0.0020 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11404 Z= 0.199 Angle : 0.600 15.076 15526 Z= 0.296 Chirality : 0.043 0.269 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.716 15.861 1538 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 15.54 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.64 (0.23), residues: 1420 helix: 2.94 (0.23), residues: 432 sheet: 0.98 (0.24), residues: 466 loop : -0.42 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 167 HIS 0.003 0.001 HIS B 70 PHE 0.029 0.002 PHE A 149 TYR 0.013 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.6976 (mmm) cc_final: 0.6698 (mmm) REVERT: C 158 GLU cc_start: 0.7731 (tp30) cc_final: 0.7230 (tp30) REVERT: C 179 MET cc_start: 0.7599 (tpt) cc_final: 0.7172 (tpt) REVERT: E 178 ASP cc_start: 0.7696 (t70) cc_final: 0.7420 (t0) REVERT: D 154 ILE cc_start: 0.7635 (mm) cc_final: 0.7416 (mt) REVERT: B 50 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7373 (m-80) outliers start: 34 outliers final: 30 residues processed: 206 average time/residue: 0.2124 time to fit residues: 63.8336 Evaluate side-chains 213 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.062849 restraints weight = 25753.132| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.68 r_work: 0.2784 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11404 Z= 0.209 Angle : 0.599 15.156 15526 Z= 0.297 Chirality : 0.043 0.250 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.724 15.894 1538 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.50 % Allowed : 15.78 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.62 (0.23), residues: 1420 helix: 2.95 (0.23), residues: 432 sheet: 0.96 (0.24), residues: 466 loop : -0.44 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 167 HIS 0.003 0.001 HIS A 325 PHE 0.031 0.002 PHE B 120 TYR 0.012 0.001 TYR C 53 ARG 0.004 0.000 ARG A 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.55 seconds wall clock time: 47 minutes 18.75 seconds (2838.75 seconds total)