Starting phenix.real_space_refine on Mon Mar 11 15:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjl_33231/03_2024/7xjl_33231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjl_33231/03_2024/7xjl_33231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjl_33231/03_2024/7xjl_33231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjl_33231/03_2024/7xjl_33231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjl_33231/03_2024/7xjl_33231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjl_33231/03_2024/7xjl_33231.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.090 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 54 5.16 5 C 5453 2.51 5 N 1456 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8527 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 109 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 12} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1750 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 98 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2132 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 5.18, per 1000 atoms: 0.61 Number of scatterers: 8527 At special positions: 0 Unit cell: (92.395, 119.57, 118.483, 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 54 16.00 O 1564 8.00 N 1456 7.00 C 5453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.757A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.557A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.512A pdb=" N LEU B 134 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.895A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 183 through 203 Processing helix chain 'B' and resid 222 through 243 removed outlier: 4.139A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.654A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.731A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.534A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.767A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.563A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.508A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 24 through 53 Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 58 through 88 Proline residue: F 80 - end of helix removed outlier: 4.786A pdb=" N ILE F 85 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 129 removed outlier: 4.163A pdb=" N LEU F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS F 98 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS F 102 " --> pdb=" O CYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.807A pdb=" N GLU F 135 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.793A pdb=" N ALA F 186 " --> pdb=" O PRO F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 215 Processing helix chain 'F' and resid 225 through 261 removed outlier: 3.811A pdb=" N TRP F 249 " --> pdb=" O PHE F 245 " (cutoff:3.500A) Proline residue: F 251 - end of helix Processing helix chain 'F' and resid 267 through 293 removed outlier: 3.863A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 307 removed outlier: 4.032A pdb=" N THR F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE F 306 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS F 307 " --> pdb=" O PHE F 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.848A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 4.112A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.665A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105 removed outlier: 3.740A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 113 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 148 through 151 removed outlier: 5.947A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 3.660A pdb=" N GLY C 202 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.703A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 252 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.016A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.849A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.279A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.613A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 164 through 169 469 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 3.77 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: 2759 1.34 - 1.46: 2106 1.46 - 1.58: 3777 1.58 - 1.70: 0 1.70 - 1.81: 74 Bond restraints: 8716 Sorted by residual: bond pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.02e+00 bond pdb=" CG1 ILE F 64 " pdb=" CD1 ILE F 64 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.81e-01 bond pdb=" CB ASP F 71 " pdb=" CG ASP F 71 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.28e-01 bond pdb=" CB LYS A 11 " pdb=" CG LYS A 11 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.17e-01 bond pdb=" CA ASN C 313 " pdb=" C ASN C 313 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.23e-02 6.61e+03 5.93e-01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.31: 202 106.31 - 113.28: 4755 113.28 - 120.25: 2992 120.25 - 127.22: 3829 127.22 - 134.20: 99 Bond angle restraints: 11877 Sorted by residual: angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " pdb=" CG GLU C 130 " ideal model delta sigma weight residual 114.10 121.06 -6.96 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C ARG C 129 " pdb=" N GLU C 130 " pdb=" CA GLU C 130 " ideal model delta sigma weight residual 121.54 126.46 -4.92 1.91e+00 2.74e-01 6.63e+00 angle pdb=" CB LYS A 11 " pdb=" CG LYS A 11 " pdb=" CD LYS A 11 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.88e+00 angle pdb=" CA LYS B 73 " pdb=" CB LYS B 73 " pdb=" CG LYS B 73 " ideal model delta sigma weight residual 114.10 118.95 -4.85 2.00e+00 2.50e-01 5.87e+00 ... (remaining 11872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4611 17.69 - 35.38: 390 35.38 - 53.06: 69 53.06 - 70.75: 10 70.75 - 88.44: 5 Dihedral angle restraints: 5085 sinusoidal: 1795 harmonic: 3290 Sorted by residual: dihedral pdb=" CA LYS B 73 " pdb=" C LYS B 73 " pdb=" N PHE B 74 " pdb=" CA PHE B 74 " ideal model delta harmonic sigma weight residual 180.00 152.15 27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLY B 181 " pdb=" C GLY B 181 " pdb=" N ASP B 182 " pdb=" CA ASP B 182 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU C 138 " pdb=" CG GLU C 138 " pdb=" CD GLU C 138 " pdb=" OE1 GLU C 138 " ideal model delta sinusoidal sigma weight residual 0.00 -88.44 88.44 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 889 0.032 - 0.064: 324 0.064 - 0.095: 104 0.095 - 0.127: 57 0.127 - 0.159: 8 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA GLU C 130 " pdb=" N GLU C 130 " pdb=" C GLU C 130 " pdb=" CB GLU C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CG LEU F 72 " pdb=" CB LEU F 72 " pdb=" CD1 LEU F 72 " pdb=" CD2 LEU F 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA THR F 87 " pdb=" N THR F 87 " pdb=" C THR F 87 " pdb=" CB THR F 87 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1379 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " -0.015 2.00e-02 2.50e+03 1.49e-02 5.54e+00 pdb=" CG TRP C 332 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 3 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 4 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 69 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C VAL F 69 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL F 69 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA F 70 " 0.012 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 266 2.71 - 3.26: 8531 3.26 - 3.81: 14009 3.81 - 4.35: 16871 4.35 - 4.90: 28921 Nonbonded interactions: 68598 Sorted by model distance: nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.168 2.440 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.178 2.440 nonbonded pdb=" OG SER C 281 " pdb=" O HIS D 44 " model vdw 2.205 2.440 nonbonded pdb=" NZ LYS B 95 " pdb=" OD2 ASP C 228 " model vdw 2.230 2.520 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.252 2.440 ... (remaining 68593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 1.820 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 0.034 8716 Z= 0.160 Angle : 0.607 7.758 11877 Z= 0.327 Chirality : 0.041 0.159 1382 Planarity : 0.004 0.055 1504 Dihedral : 13.569 88.438 2957 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.78 (0.25), residues: 1115 helix: 2.17 (0.26), residues: 401 sheet: 0.49 (0.31), residues: 272 loop : -1.04 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 332 HIS 0.008 0.001 HIS B 82 PHE 0.020 0.002 PHE B 74 TYR 0.013 0.001 TYR B 191 ARG 0.009 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8816 (t80) cc_final: 0.8449 (t80) REVERT: B 73 LYS cc_start: 0.8376 (mmtm) cc_final: 0.7713 (pttm) REVERT: B 122 LEU cc_start: 0.8967 (mt) cc_final: 0.8647 (mp) REVERT: B 232 LYS cc_start: 0.8886 (tttp) cc_final: 0.8627 (tttp) REVERT: C 289 TYR cc_start: 0.8566 (m-80) cc_final: 0.8236 (m-80) REVERT: C 301 LYS cc_start: 0.8592 (mmpt) cc_final: 0.8138 (mmmt) REVERT: E 96 CYS cc_start: 0.8086 (t) cc_final: 0.7407 (t) REVERT: E 98 ARG cc_start: 0.8524 (ptm160) cc_final: 0.7856 (ptm160) REVERT: E 190 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7514 (ptp90) REVERT: E 192 SER cc_start: 0.7065 (t) cc_final: 0.6830 (t) REVERT: E 218 MET cc_start: 0.7594 (tmm) cc_final: 0.6614 (tmm) REVERT: F 55 GLN cc_start: 0.8187 (mp10) cc_final: 0.7974 (mp10) REVERT: F 244 LEU cc_start: 0.8064 (tp) cc_final: 0.7850 (tt) REVERT: F 305 THR cc_start: 0.7514 (m) cc_final: 0.7127 (m) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1938 time to fit residues: 70.6490 Evaluate side-chains 227 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN F 102 HIS ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 8716 Z= 0.547 Angle : 0.763 10.696 11877 Z= 0.399 Chirality : 0.049 0.210 1382 Planarity : 0.005 0.059 1504 Dihedral : 4.573 35.114 1222 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.01 % Allowed : 14.34 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.43 (0.25), residues: 1115 helix: 1.74 (0.26), residues: 404 sheet: 0.26 (0.32), residues: 263 loop : -1.06 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 211 HIS 0.007 0.002 HIS C 91 PHE 0.023 0.003 PHE F 303 TYR 0.028 0.003 TYR F 163 ARG 0.007 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9209 (t80) cc_final: 0.8434 (t80) REVERT: B 73 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8022 (pttm) REVERT: B 185 ARG cc_start: 0.7851 (ptt-90) cc_final: 0.7522 (ptt-90) REVERT: C 101 MET cc_start: 0.8368 (mtm) cc_final: 0.8075 (ptp) REVERT: C 153 ASP cc_start: 0.7687 (m-30) cc_final: 0.7437 (m-30) REVERT: C 264 TYR cc_start: 0.8541 (m-10) cc_final: 0.8275 (m-80) REVERT: C 301 LYS cc_start: 0.8368 (mmpt) cc_final: 0.7951 (mmmt) REVERT: E 96 CYS cc_start: 0.8161 (t) cc_final: 0.7860 (t) REVERT: E 143 VAL cc_start: 0.8415 (t) cc_final: 0.8191 (m) REVERT: E 177 ILE cc_start: 0.8775 (tp) cc_final: 0.8529 (tp) REVERT: E 180 MET cc_start: 0.7454 (ptt) cc_final: 0.7023 (ptt) REVERT: E 218 MET cc_start: 0.8326 (tmm) cc_final: 0.7938 (tmm) REVERT: F 129 TYR cc_start: 0.8539 (m-10) cc_final: 0.8200 (m-10) REVERT: F 172 LEU cc_start: 0.9025 (mt) cc_final: 0.8807 (mt) REVERT: F 237 MET cc_start: 0.8594 (mmm) cc_final: 0.7893 (mmt) outliers start: 26 outliers final: 21 residues processed: 234 average time/residue: 0.1910 time to fit residues: 61.7534 Evaluate side-chains 227 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8716 Z= 0.200 Angle : 0.583 9.785 11877 Z= 0.299 Chirality : 0.043 0.146 1382 Planarity : 0.004 0.048 1504 Dihedral : 4.363 32.807 1222 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.93 % Allowed : 17.46 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.77 (0.25), residues: 1115 helix: 2.29 (0.26), residues: 390 sheet: 0.32 (0.32), residues: 261 loop : -0.94 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.004 0.001 HIS F 102 PHE 0.026 0.002 PHE F 303 TYR 0.024 0.002 TYR F 164 ARG 0.003 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 237 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9142 (t80) cc_final: 0.8617 (t80) REVERT: B 73 LYS cc_start: 0.8604 (mmtm) cc_final: 0.7930 (pttm) REVERT: B 185 ARG cc_start: 0.7821 (ptt-90) cc_final: 0.7507 (ptt-90) REVERT: C 153 ASP cc_start: 0.7517 (m-30) cc_final: 0.7255 (m-30) REVERT: C 289 TYR cc_start: 0.8804 (m-80) cc_final: 0.8580 (m-80) REVERT: C 301 LYS cc_start: 0.8277 (mmpt) cc_final: 0.7840 (mmmt) REVERT: E 96 CYS cc_start: 0.8271 (t) cc_final: 0.7785 (t) REVERT: E 177 ILE cc_start: 0.8750 (tp) cc_final: 0.8405 (tp) REVERT: E 180 MET cc_start: 0.7384 (ptt) cc_final: 0.7029 (ptt) REVERT: E 190 ARG cc_start: 0.8098 (ptp-170) cc_final: 0.7529 (ptp90) REVERT: E 218 MET cc_start: 0.8305 (tmm) cc_final: 0.7961 (tmm) REVERT: F 82 GLN cc_start: 0.8143 (tt0) cc_final: 0.7850 (tt0) REVERT: F 129 TYR cc_start: 0.8608 (m-10) cc_final: 0.8131 (m-10) REVERT: F 237 MET cc_start: 0.8586 (mmm) cc_final: 0.8101 (mmt) REVERT: F 244 LEU cc_start: 0.8611 (tp) cc_final: 0.8366 (tt) REVERT: F 275 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9152 (tp) outliers start: 34 outliers final: 20 residues processed: 251 average time/residue: 0.1932 time to fit residues: 67.7865 Evaluate side-chains 244 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 223 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 281 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 44 HIS ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8716 Z= 0.229 Angle : 0.580 12.841 11877 Z= 0.296 Chirality : 0.042 0.174 1382 Planarity : 0.004 0.052 1504 Dihedral : 4.295 32.419 1222 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.05 % Allowed : 19.19 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.80 (0.25), residues: 1115 helix: 2.29 (0.26), residues: 394 sheet: 0.33 (0.32), residues: 261 loop : -0.92 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 297 HIS 0.002 0.001 HIS B 209 PHE 0.024 0.002 PHE E 27 TYR 0.018 0.002 TYR F 213 ARG 0.004 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9142 (t80) cc_final: 0.8670 (t80) REVERT: B 73 LYS cc_start: 0.8614 (mmtm) cc_final: 0.7936 (pttm) REVERT: C 153 ASP cc_start: 0.7551 (m-30) cc_final: 0.7265 (m-30) REVERT: C 301 LYS cc_start: 0.8272 (mmpt) cc_final: 0.7845 (mmmt) REVERT: E 96 CYS cc_start: 0.8274 (t) cc_final: 0.7850 (t) REVERT: E 143 VAL cc_start: 0.8408 (t) cc_final: 0.8193 (m) REVERT: E 148 ARG cc_start: 0.8159 (mmt180) cc_final: 0.6933 (mtm110) REVERT: E 177 ILE cc_start: 0.8645 (tp) cc_final: 0.8249 (tp) REVERT: E 180 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7028 (ptt) REVERT: E 190 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7435 (ptp90) REVERT: E 218 MET cc_start: 0.8284 (tmm) cc_final: 0.7914 (tmm) REVERT: F 129 TYR cc_start: 0.8607 (m-10) cc_final: 0.8167 (m-10) REVERT: F 237 MET cc_start: 0.8652 (mmm) cc_final: 0.8096 (mmt) REVERT: F 275 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9148 (tp) outliers start: 35 outliers final: 26 residues processed: 234 average time/residue: 0.1927 time to fit residues: 62.4827 Evaluate side-chains 240 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 281 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 340 ASN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8716 Z= 0.330 Angle : 0.641 20.883 11877 Z= 0.322 Chirality : 0.044 0.254 1382 Planarity : 0.004 0.049 1504 Dihedral : 4.445 38.297 1222 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 6.36 % Allowed : 19.08 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.66 (0.25), residues: 1115 helix: 2.10 (0.26), residues: 396 sheet: 0.30 (0.32), residues: 263 loop : -0.99 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 297 HIS 0.004 0.001 HIS B 209 PHE 0.023 0.002 PHE E 27 TYR 0.024 0.002 TYR F 213 ARG 0.007 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 224 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9218 (t80) cc_final: 0.8712 (t80) REVERT: B 73 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8017 (pttm) REVERT: C 153 ASP cc_start: 0.7670 (m-30) cc_final: 0.7372 (m-30) REVERT: C 237 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7445 (p0) REVERT: C 301 LYS cc_start: 0.8265 (mmpt) cc_final: 0.7842 (mmmt) REVERT: E 96 CYS cc_start: 0.8370 (t) cc_final: 0.7877 (t) REVERT: E 143 VAL cc_start: 0.8394 (t) cc_final: 0.8170 (m) REVERT: E 148 ARG cc_start: 0.8293 (mmt180) cc_final: 0.6936 (mtm110) REVERT: E 177 ILE cc_start: 0.8506 (tp) cc_final: 0.8050 (tp) REVERT: E 180 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7085 (ptt) REVERT: E 190 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7378 (ptp90) REVERT: E 219 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8508 (tm-30) REVERT: F 129 TYR cc_start: 0.8679 (m-10) cc_final: 0.8304 (m-10) REVERT: F 237 MET cc_start: 0.8750 (mmm) cc_final: 0.8160 (mmt) REVERT: F 275 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9191 (tp) outliers start: 55 outliers final: 43 residues processed: 257 average time/residue: 0.1917 time to fit residues: 68.5494 Evaluate side-chains 267 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 286 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8716 Z= 0.168 Angle : 0.576 13.998 11877 Z= 0.289 Chirality : 0.042 0.225 1382 Planarity : 0.004 0.052 1504 Dihedral : 4.301 34.994 1222 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.16 % Allowed : 21.62 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.83 (0.25), residues: 1115 helix: 2.31 (0.26), residues: 394 sheet: 0.28 (0.32), residues: 273 loop : -0.88 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 332 HIS 0.002 0.001 HIS B 209 PHE 0.024 0.002 PHE E 27 TYR 0.023 0.001 TYR F 213 ARG 0.009 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9150 (t80) cc_final: 0.8832 (t80) REVERT: B 73 LYS cc_start: 0.8536 (mmtm) cc_final: 0.7907 (pttm) REVERT: C 153 ASP cc_start: 0.7575 (m-30) cc_final: 0.7291 (m-30) REVERT: C 237 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7386 (p0) REVERT: C 301 LYS cc_start: 0.8340 (mmpt) cc_final: 0.8036 (mmmt) REVERT: E 34 MET cc_start: 0.8214 (mmm) cc_final: 0.7778 (mmp) REVERT: E 96 CYS cc_start: 0.8234 (t) cc_final: 0.7439 (t) REVERT: E 148 ARG cc_start: 0.8220 (mmt180) cc_final: 0.6963 (mtm110) REVERT: E 177 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8148 (tp) REVERT: E 180 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7177 (ptt) REVERT: E 190 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.7339 (ptp90) REVERT: E 219 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8580 (tm-30) REVERT: F 82 GLN cc_start: 0.8119 (tt0) cc_final: 0.7863 (tt0) REVERT: F 129 TYR cc_start: 0.8648 (m-80) cc_final: 0.8242 (m-10) REVERT: F 237 MET cc_start: 0.8673 (mmm) cc_final: 0.8197 (mmt) REVERT: F 275 ILE cc_start: 0.9501 (mm) cc_final: 0.9155 (tp) outliers start: 36 outliers final: 29 residues processed: 251 average time/residue: 0.1843 time to fit residues: 64.9731 Evaluate side-chains 261 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 286 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8716 Z= 0.235 Angle : 0.589 14.553 11877 Z= 0.298 Chirality : 0.042 0.175 1382 Planarity : 0.004 0.047 1504 Dihedral : 4.283 35.986 1222 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.74 % Allowed : 22.31 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.84 (0.25), residues: 1115 helix: 2.31 (0.26), residues: 394 sheet: 0.37 (0.32), residues: 268 loop : -0.93 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 332 HIS 0.003 0.001 HIS B 209 PHE 0.026 0.002 PHE E 27 TYR 0.019 0.002 TYR B 115 ARG 0.007 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9196 (t80) cc_final: 0.8845 (t80) REVERT: B 73 LYS cc_start: 0.8571 (mmtm) cc_final: 0.7924 (pttm) REVERT: B 166 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8269 (mm-30) REVERT: C 153 ASP cc_start: 0.7623 (m-30) cc_final: 0.7352 (m-30) REVERT: C 237 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7435 (p0) REVERT: C 301 LYS cc_start: 0.8327 (mmpt) cc_final: 0.7917 (mmmt) REVERT: E 98 ARG cc_start: 0.8385 (ptm160) cc_final: 0.8055 (ptm160) REVERT: E 148 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7000 (mtm110) REVERT: E 177 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8087 (tp) REVERT: E 180 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7126 (ptt) REVERT: E 190 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.7356 (ptp90) REVERT: F 82 GLN cc_start: 0.8116 (tt0) cc_final: 0.7886 (tt0) REVERT: F 129 TYR cc_start: 0.8646 (m-80) cc_final: 0.8267 (m-10) REVERT: F 237 MET cc_start: 0.8707 (mmm) cc_final: 0.8193 (mmt) REVERT: F 275 ILE cc_start: 0.9513 (mm) cc_final: 0.9170 (tp) outliers start: 41 outliers final: 36 residues processed: 247 average time/residue: 0.1873 time to fit residues: 64.3984 Evaluate side-chains 260 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 286 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS E 174 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8716 Z= 0.181 Angle : 0.608 19.015 11877 Z= 0.299 Chirality : 0.042 0.196 1382 Planarity : 0.004 0.046 1504 Dihedral : 4.217 33.438 1222 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.51 % Allowed : 23.24 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1115 helix: 2.40 (0.26), residues: 388 sheet: 0.35 (0.31), residues: 280 loop : -0.84 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP F 260 HIS 0.002 0.001 HIS B 209 PHE 0.026 0.002 PHE E 27 TYR 0.026 0.002 TYR F 164 ARG 0.007 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9146 (t80) cc_final: 0.8797 (t80) REVERT: B 73 LYS cc_start: 0.8512 (mmtm) cc_final: 0.7879 (pttm) REVERT: C 103 CYS cc_start: 0.7790 (p) cc_final: 0.7492 (p) REVERT: C 153 ASP cc_start: 0.7592 (m-30) cc_final: 0.7280 (m-30) REVERT: C 237 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7327 (p0) REVERT: C 301 LYS cc_start: 0.8462 (mmpt) cc_final: 0.8192 (mmmt) REVERT: E 34 MET cc_start: 0.8108 (mmm) cc_final: 0.7763 (mmm) REVERT: E 98 ARG cc_start: 0.8367 (ptm160) cc_final: 0.8088 (ptm160) REVERT: E 148 ARG cc_start: 0.8240 (mmt180) cc_final: 0.6994 (mtm110) REVERT: E 177 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8143 (tp) REVERT: E 180 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7201 (ptt) REVERT: E 190 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7351 (ptp90) REVERT: E 219 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8729 (tm-30) REVERT: F 82 GLN cc_start: 0.8105 (tt0) cc_final: 0.7878 (tt0) REVERT: F 129 TYR cc_start: 0.8617 (m-80) cc_final: 0.8278 (m-10) REVERT: F 237 MET cc_start: 0.8667 (mmm) cc_final: 0.8180 (mmt) REVERT: F 275 ILE cc_start: 0.9497 (mm) cc_final: 0.9149 (tp) outliers start: 39 outliers final: 29 residues processed: 249 average time/residue: 0.2035 time to fit residues: 69.9155 Evaluate side-chains 258 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 286 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8716 Z= 0.191 Angle : 0.625 22.392 11877 Z= 0.306 Chirality : 0.044 0.442 1382 Planarity : 0.004 0.046 1504 Dihedral : 4.151 31.650 1222 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.05 % Allowed : 24.39 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.94 (0.25), residues: 1115 helix: 2.42 (0.26), residues: 388 sheet: 0.43 (0.32), residues: 271 loop : -0.86 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 260 HIS 0.003 0.001 HIS F 110 PHE 0.025 0.002 PHE E 27 TYR 0.021 0.002 TYR F 164 ARG 0.008 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 226 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9132 (t80) cc_final: 0.8803 (t80) REVERT: B 73 LYS cc_start: 0.8559 (mmtm) cc_final: 0.7823 (pttm) REVERT: C 153 ASP cc_start: 0.7623 (m-30) cc_final: 0.7283 (m-30) REVERT: C 237 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7391 (p0) REVERT: C 301 LYS cc_start: 0.8473 (mmpt) cc_final: 0.8270 (mmmt) REVERT: E 34 MET cc_start: 0.8087 (mmm) cc_final: 0.7667 (mmm) REVERT: E 97 VAL cc_start: 0.8482 (t) cc_final: 0.8275 (t) REVERT: E 98 ARG cc_start: 0.8365 (ptm160) cc_final: 0.8097 (ptm160) REVERT: E 111 TRP cc_start: 0.8128 (m100) cc_final: 0.7898 (m-10) REVERT: E 148 ARG cc_start: 0.8197 (mmt180) cc_final: 0.6901 (mtm110) REVERT: E 177 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8104 (tp) REVERT: E 180 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7088 (ptt) REVERT: E 190 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.7347 (ptp90) REVERT: E 219 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8665 (tm-30) REVERT: F 82 GLN cc_start: 0.8068 (tt0) cc_final: 0.7845 (tt0) REVERT: F 109 MET cc_start: 0.8082 (ttt) cc_final: 0.7463 (ttt) REVERT: F 129 TYR cc_start: 0.8577 (m-80) cc_final: 0.8289 (m-10) REVERT: F 185 ARG cc_start: 0.7043 (ttm110) cc_final: 0.6822 (ttm110) REVERT: F 237 MET cc_start: 0.8664 (mmm) cc_final: 0.8165 (mmt) REVERT: F 275 ILE cc_start: 0.9493 (mm) cc_final: 0.9139 (tp) outliers start: 35 outliers final: 28 residues processed: 244 average time/residue: 0.1969 time to fit residues: 65.7084 Evaluate side-chains 247 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 286 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 0.2980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8716 Z= 0.173 Angle : 0.626 21.372 11877 Z= 0.304 Chirality : 0.044 0.442 1382 Planarity : 0.004 0.046 1504 Dihedral : 4.080 28.520 1222 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.24 % Allowed : 24.97 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.91 (0.25), residues: 1115 helix: 2.35 (0.26), residues: 389 sheet: 0.44 (0.32), residues: 269 loop : -0.83 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 260 HIS 0.002 0.000 HIS B 209 PHE 0.025 0.002 PHE E 27 TYR 0.020 0.001 TYR F 164 ARG 0.009 0.000 ARG B 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9088 (t80) cc_final: 0.8781 (t80) REVERT: B 73 LYS cc_start: 0.8531 (mmtm) cc_final: 0.7798 (pttm) REVERT: B 163 TYR cc_start: 0.8323 (m-80) cc_final: 0.8116 (m-80) REVERT: C 153 ASP cc_start: 0.7540 (m-30) cc_final: 0.7201 (m-30) REVERT: C 237 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7382 (p0) REVERT: E 34 MET cc_start: 0.7954 (mmm) cc_final: 0.7541 (mmm) REVERT: E 98 ARG cc_start: 0.8357 (ptm160) cc_final: 0.8103 (ptm160) REVERT: E 148 ARG cc_start: 0.8212 (mmt180) cc_final: 0.6932 (mtm110) REVERT: E 177 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8071 (tp) REVERT: E 180 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7050 (ptt) REVERT: E 190 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7347 (ptp90) REVERT: F 109 MET cc_start: 0.8041 (ttt) cc_final: 0.7449 (ttt) REVERT: F 237 MET cc_start: 0.8609 (mmm) cc_final: 0.8115 (mmt) REVERT: F 275 ILE cc_start: 0.9486 (mm) cc_final: 0.9140 (tp) outliers start: 28 outliers final: 21 residues processed: 236 average time/residue: 0.2039 time to fit residues: 66.5978 Evaluate side-chains 241 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 286 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120804 restraints weight = 12864.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125028 restraints weight = 6798.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127752 restraints weight = 4563.876| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8716 Z= 0.192 Angle : 0.640 21.606 11877 Z= 0.312 Chirality : 0.044 0.451 1382 Planarity : 0.004 0.046 1504 Dihedral : 4.081 28.335 1222 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.35 % Allowed : 25.55 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.89 (0.25), residues: 1115 helix: 2.35 (0.26), residues: 388 sheet: 0.41 (0.32), residues: 269 loop : -0.86 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 260 HIS 0.002 0.001 HIS B 209 PHE 0.024 0.002 PHE E 27 TYR 0.025 0.002 TYR F 213 ARG 0.007 0.000 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.27 seconds wall clock time: 38 minutes 15.81 seconds (2295.81 seconds total)