Starting phenix.real_space_refine on Wed Feb 14 03:56:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjk_33230/02_2024/7xjk_33230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjk_33230/02_2024/7xjk_33230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjk_33230/02_2024/7xjk_33230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjk_33230/02_2024/7xjk_33230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjk_33230/02_2024/7xjk_33230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjk_33230/02_2024/7xjk_33230.pdb" } resolution = 3.3 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= 0.115 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 53 5.16 5 C 5478 2.51 5 N 1472 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 25": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8570 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 112 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 14} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 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': 7} Unresolved non-hydrogen planarities: 93 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: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2166 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 5.67, per 1000 atoms: 0.66 Number of scatterers: 8570 At special positions: 0 Unit cell: (91.308, 119.57, 120.657, 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 53 16.00 O 1567 8.00 N 1472 7.00 C 5478 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=2.04 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: 3.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 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: 28 helices and 14 sheets defined 38.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.956A 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 204 removed outlier: 3.533A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 4.045A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.693A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.505A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.803A 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: 4.092A 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: 4.073A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 53 Processing helix chain 'F' and resid 58 through 88 Proline residue: F 80 - end of helix Processing helix chain 'F' and resid 95 through 129 removed outlier: 3.505A pdb=" N LYS F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS F 102 " --> pdb=" O CYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 138 through 157 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 180 through 196 Processing helix chain 'F' and resid 196 through 215 Processing helix chain 'F' and resid 225 through 262 removed outlier: 4.196A 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: 3.912A 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 Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.942A pdb=" N PHE B 84 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.411A 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: 3.666A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 63 removed outlier: 6.546A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.702A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.756A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.955A 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 192 removed outlier: 3.844A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.398A 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: 6.403A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.950A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (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 58 through 60 removed outlier: 5.156A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.463A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.115A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 164 through 169 459 hydrogen bonds defined for protein. 1308 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: 2.38 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2772 1.34 - 1.46: 2196 1.46 - 1.58: 3719 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8759 Sorted by residual: bond pdb=" CB ASN F 43 " pdb=" CG ASN F 43 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.90e+00 bond pdb=" C VAL F 79 " pdb=" N PRO F 80 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.44e-02 4.82e+03 3.16e+00 bond pdb=" N LEU F 72 " pdb=" CA LEU F 72 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.24e-02 6.50e+03 3.11e+00 bond pdb=" CA ASP F 71 " pdb=" C ASP F 71 " ideal model delta sigma weight residual 1.524 1.506 0.017 1.27e-02 6.20e+03 1.86e+00 bond pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.67e+00 ... (remaining 8754 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 192 106.34 - 113.26: 4832 113.26 - 120.17: 2999 120.17 - 127.09: 3803 127.09 - 134.01: 102 Bond angle restraints: 11928 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 109.28 4.43 9.50e-01 1.11e+00 2.17e+01 angle pdb=" N HIS F 176 " pdb=" CA HIS F 176 " pdb=" C HIS F 176 " ideal model delta sigma weight residual 108.25 113.56 -5.31 1.16e+00 7.43e-01 2.10e+01 angle pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " pdb=" CG GLU C 130 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.54e+00 angle pdb=" CA TYR F 163 " pdb=" CB TYR F 163 " pdb=" CG TYR F 163 " ideal model delta sigma weight residual 113.90 118.40 -4.50 1.80e+00 3.09e-01 6.26e+00 angle pdb=" CA ILE C 270 " pdb=" C ILE C 270 " pdb=" N CYS C 271 " ideal model delta sigma weight residual 119.87 116.52 3.35 1.34e+00 5.57e-01 6.24e+00 ... (remaining 11923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4636 17.90 - 35.80: 408 35.80 - 53.69: 62 53.69 - 71.59: 6 71.59 - 89.49: 4 Dihedral angle restraints: 5116 sinusoidal: 1824 harmonic: 3292 Sorted by residual: dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASP F 71 " pdb=" C ASP F 71 " pdb=" N LEU F 72 " pdb=" CA LEU F 72 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 81 " pdb=" C PHE B 81 " pdb=" N HIS B 82 " pdb=" CA HIS B 82 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1011 0.045 - 0.090: 288 0.090 - 0.134: 78 0.134 - 0.179: 5 0.179 - 0.224: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CG LEU F 76 " pdb=" CB LEU F 76 " pdb=" CD1 LEU F 76 " pdb=" CD2 LEU F 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 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 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU F 76 " pdb=" N LEU F 76 " pdb=" C LEU F 76 " pdb=" CB LEU F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1381 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO D 49 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 69 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C VAL F 69 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL F 69 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA F 70 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 194 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C PHE F 194 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE F 194 " 0.015 2.00e-02 2.50e+03 pdb=" N SER F 195 " 0.014 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 385 2.72 - 3.26: 8667 3.26 - 3.81: 14226 3.81 - 4.35: 17066 4.35 - 4.90: 30039 Nonbonded interactions: 70383 Sorted by model distance: nonbonded pdb=" OD2 ASP F 188 " pdb=" NE1 TRP F 260 " model vdw 2.172 2.520 nonbonded pdb=" O SER E 31 " pdb=" OG SER E 53 " model vdw 2.175 2.440 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.204 2.440 nonbonded pdb=" OE2 GLU C 260 " pdb=" OG1 THR C 263 " model vdw 2.225 2.440 nonbonded pdb=" OG SER F 95 " pdb=" OE1 GLN F 166 " model vdw 2.247 2.440 ... (remaining 70378 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.830 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.430 Find NCS groups from input model: 0.230 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.005 0.049 8759 Z= 0.325 Angle : 0.651 8.197 11928 Z= 0.353 Chirality : 0.044 0.224 1384 Planarity : 0.005 0.086 1510 Dihedral : 13.522 89.491 2988 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 0.32 (0.25), residues: 1117 helix: 1.58 (0.26), residues: 399 sheet: 0.07 (0.31), residues: 264 loop : -0.90 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 179 HIS 0.009 0.001 HIS F 176 PHE 0.016 0.002 PHE E 27 TYR 0.029 0.002 TYR F 292 ARG 0.006 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.043 Fit side-chains REVERT: A 11 LEU cc_start: 0.9083 (mm) cc_final: 0.8810 (mm) REVERT: B 179 GLU cc_start: 0.5497 (pp20) cc_final: 0.5127 (pp20) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2122 time to fit residues: 47.5072 Evaluate side-chains 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8759 Z= 0.198 Angle : 0.535 7.010 11928 Z= 0.280 Chirality : 0.041 0.150 1384 Planarity : 0.004 0.051 1510 Dihedral : 4.150 26.275 1228 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.49 % Allowed : 10.08 % Favored : 88.43 % 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: 0.68 (0.25), residues: 1117 helix: 2.12 (0.26), residues: 398 sheet: 0.22 (0.33), residues: 246 loop : -0.87 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.010 0.001 HIS F 176 PHE 0.017 0.001 PHE F 81 TYR 0.019 0.002 TYR F 163 ARG 0.004 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.032 Fit side-chains REVERT: A 11 LEU cc_start: 0.8899 (mm) cc_final: 0.8604 (mm) REVERT: E 38 ARG cc_start: 0.7601 (ptp90) cc_final: 0.7151 (ptp90) REVERT: E 46 GLU cc_start: 0.7897 (pt0) cc_final: 0.7665 (mt-10) REVERT: E 202 LEU cc_start: 0.8576 (tp) cc_final: 0.8109 (tp) REVERT: F 187 MET cc_start: 0.8355 (tpp) cc_final: 0.7826 (tpp) outliers start: 13 outliers final: 9 residues processed: 151 average time/residue: 0.1991 time to fit residues: 42.0620 Evaluate side-chains 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 239 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8759 Z= 0.216 Angle : 0.525 8.543 11928 Z= 0.275 Chirality : 0.041 0.138 1384 Planarity : 0.004 0.048 1510 Dihedral : 4.058 25.213 1228 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.63 % Allowed : 13.86 % Favored : 83.51 % 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: 0.68 (0.25), residues: 1117 helix: 2.10 (0.26), residues: 399 sheet: 0.12 (0.32), residues: 259 loop : -0.82 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.009 0.001 HIS F 176 PHE 0.023 0.002 PHE F 156 TYR 0.020 0.002 TYR F 163 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 0.988 Fit side-chains REVERT: A 11 LEU cc_start: 0.8893 (mm) cc_final: 0.8581 (mm) outliers start: 23 outliers final: 16 residues processed: 156 average time/residue: 0.1991 time to fit residues: 43.2668 Evaluate side-chains 145 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.0470 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8759 Z= 0.223 Angle : 0.526 7.616 11928 Z= 0.275 Chirality : 0.041 0.139 1384 Planarity : 0.004 0.056 1510 Dihedral : 4.020 24.682 1228 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.18 % Allowed : 16.27 % Favored : 81.56 % 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: 0.70 (0.25), residues: 1117 helix: 2.11 (0.26), residues: 399 sheet: 0.08 (0.32), residues: 259 loop : -0.77 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.008 0.001 HIS F 176 PHE 0.020 0.001 PHE C 253 TYR 0.020 0.002 TYR F 163 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.986 Fit side-chains REVERT: A 11 LEU cc_start: 0.8893 (mm) cc_final: 0.8575 (mm) REVERT: E 38 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7365 (ptp90) REVERT: F 187 MET cc_start: 0.8670 (tpp) cc_final: 0.7842 (tpp) outliers start: 19 outliers final: 15 residues processed: 155 average time/residue: 0.2065 time to fit residues: 44.2606 Evaluate side-chains 147 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.0050 chunk 44 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8759 Z= 0.303 Angle : 0.568 8.313 11928 Z= 0.297 Chirality : 0.043 0.163 1384 Planarity : 0.004 0.054 1510 Dihedral : 4.227 26.827 1228 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.86 % Allowed : 17.98 % Favored : 79.15 % 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: 0.59 (0.25), residues: 1117 helix: 1.95 (0.26), residues: 399 sheet: -0.05 (0.32), residues: 259 loop : -0.70 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 179 HIS 0.008 0.001 HIS F 176 PHE 0.032 0.002 PHE F 156 TYR 0.024 0.002 TYR F 163 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.219 Fit side-chains REVERT: A 11 LEU cc_start: 0.8948 (mm) cc_final: 0.8640 (mm) REVERT: B 179 GLU cc_start: 0.5928 (pp20) cc_final: 0.5445 (pp20) REVERT: C 290 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: E 38 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7438 (ptp90) REVERT: F 187 MET cc_start: 0.8696 (tpp) cc_final: 0.7927 (tpp) outliers start: 25 outliers final: 19 residues processed: 158 average time/residue: 0.1968 time to fit residues: 43.6343 Evaluate side-chains 155 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8759 Z= 0.203 Angle : 0.530 7.417 11928 Z= 0.277 Chirality : 0.041 0.146 1384 Planarity : 0.004 0.055 1510 Dihedral : 4.062 24.459 1228 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.21 % Allowed : 19.24 % Favored : 77.55 % 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: 0.73 (0.25), residues: 1117 helix: 2.14 (0.26), residues: 399 sheet: -0.02 (0.32), residues: 260 loop : -0.67 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.007 0.001 HIS F 176 PHE 0.025 0.001 PHE F 156 TYR 0.020 0.002 TYR F 163 ARG 0.003 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.017 Fit side-chains REVERT: A 11 LEU cc_start: 0.8951 (mm) cc_final: 0.8634 (mm) REVERT: E 38 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7379 (ptp90) REVERT: F 187 MET cc_start: 0.8684 (tpp) cc_final: 0.7869 (tpp) outliers start: 28 outliers final: 20 residues processed: 158 average time/residue: 0.2041 time to fit residues: 44.7470 Evaluate side-chains 154 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.0010 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8759 Z= 0.165 Angle : 0.509 6.851 11928 Z= 0.265 Chirality : 0.040 0.148 1384 Planarity : 0.004 0.047 1510 Dihedral : 3.849 22.593 1228 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.86 % Allowed : 20.05 % Favored : 77.09 % 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 (0.26), residues: 1117 helix: 2.32 (0.26), residues: 399 sheet: 0.09 (0.32), residues: 263 loop : -0.65 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.006 0.001 HIS F 176 PHE 0.020 0.001 PHE C 253 TYR 0.017 0.001 TYR F 163 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.999 Fit side-chains REVERT: A 11 LEU cc_start: 0.8946 (mm) cc_final: 0.8645 (mm) REVERT: B 179 GLU cc_start: 0.5998 (pp20) cc_final: 0.5553 (pp20) REVERT: E 38 ARG cc_start: 0.7535 (ptp90) cc_final: 0.7250 (ptp90) REVERT: F 187 MET cc_start: 0.8648 (tpp) cc_final: 0.7903 (tpp) outliers start: 25 outliers final: 21 residues processed: 164 average time/residue: 0.2020 time to fit residues: 46.1384 Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8759 Z= 0.173 Angle : 0.519 6.716 11928 Z= 0.269 Chirality : 0.040 0.155 1384 Planarity : 0.004 0.046 1510 Dihedral : 3.827 22.171 1228 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.32 % Allowed : 20.16 % Favored : 76.52 % 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 (0.26), residues: 1117 helix: 2.37 (0.26), residues: 399 sheet: 0.09 (0.32), residues: 260 loop : -0.68 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.018 0.001 PHE C 253 TYR 0.018 0.001 TYR F 129 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 0.987 Fit side-chains REVERT: A 11 LEU cc_start: 0.8936 (mm) cc_final: 0.8619 (mm) REVERT: B 179 GLU cc_start: 0.5984 (pp20) cc_final: 0.5525 (pp20) REVERT: E 38 ARG cc_start: 0.7595 (ptp90) cc_final: 0.7306 (ptp90) REVERT: F 187 MET cc_start: 0.8707 (tpp) cc_final: 0.7962 (tpp) outliers start: 29 outliers final: 25 residues processed: 162 average time/residue: 0.1970 time to fit residues: 44.5176 Evaluate side-chains 162 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER 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: 4.9990 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 0.0000 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.0060 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8759 Z= 0.141 Angle : 0.510 7.294 11928 Z= 0.263 Chirality : 0.040 0.154 1384 Planarity : 0.003 0.039 1510 Dihedral : 3.686 20.132 1228 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.29 % Allowed : 21.99 % Favored : 75.72 % 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: 1.02 (0.26), residues: 1117 helix: 2.46 (0.26), residues: 399 sheet: 0.09 (0.31), residues: 277 loop : -0.57 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.018 0.001 PHE C 253 TYR 0.014 0.001 TYR F 163 ARG 0.004 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8959 (mm) cc_final: 0.8655 (mm) REVERT: B 166 GLU cc_start: 0.7953 (pm20) cc_final: 0.7618 (pm20) REVERT: B 179 GLU cc_start: 0.5972 (pp20) cc_final: 0.5597 (pp20) REVERT: E 38 ARG cc_start: 0.7502 (ptp90) cc_final: 0.7224 (ptp90) REVERT: F 187 MET cc_start: 0.8703 (tpp) cc_final: 0.7965 (tpp) outliers start: 20 outliers final: 17 residues processed: 163 average time/residue: 0.2055 time to fit residues: 47.0156 Evaluate side-chains 157 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8759 Z= 0.166 Angle : 0.532 8.809 11928 Z= 0.274 Chirality : 0.041 0.202 1384 Planarity : 0.004 0.038 1510 Dihedral : 3.701 20.646 1228 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.06 % Allowed : 23.60 % Favored : 74.34 % 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: 1.01 (0.26), residues: 1117 helix: 2.43 (0.26), residues: 399 sheet: 0.12 (0.31), residues: 277 loop : -0.59 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.021 0.001 PHE C 253 TYR 0.018 0.001 TYR F 129 ARG 0.006 0.000 ARG E 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8949 (mm) cc_final: 0.8638 (mm) REVERT: B 120 GLU cc_start: 0.7759 (pp20) cc_final: 0.7380 (pp20) REVERT: B 166 GLU cc_start: 0.7957 (pm20) cc_final: 0.7615 (pm20) REVERT: B 179 GLU cc_start: 0.5968 (pp20) cc_final: 0.5572 (pp20) REVERT: E 38 ARG cc_start: 0.7489 (ptp90) cc_final: 0.7206 (ptp90) REVERT: F 165 GLN cc_start: 0.6406 (tt0) cc_final: 0.6204 (tt0) REVERT: F 187 MET cc_start: 0.8683 (tpp) cc_final: 0.7990 (tpp) outliers start: 18 outliers final: 18 residues processed: 150 average time/residue: 0.2050 time to fit residues: 42.7363 Evaluate side-chains 161 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 30.0000 chunk 13 optimal weight: 0.0670 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** 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 = 0.4178 r_free = 0.4178 target = 0.187822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148042 restraints weight = 10536.290| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.15 r_work: 0.3603 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8759 Z= 0.143 Angle : 0.519 8.891 11928 Z= 0.267 Chirality : 0.040 0.198 1384 Planarity : 0.003 0.032 1510 Dihedral : 3.603 19.690 1228 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 23.60 % Favored : 74.11 % 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: 1.04 (0.26), residues: 1117 helix: 2.48 (0.26), residues: 399 sheet: 0.19 (0.32), residues: 277 loop : -0.64 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.020 0.001 PHE C 253 TYR 0.014 0.001 TYR F 163 ARG 0.007 0.000 ARG E 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.40 seconds wall clock time: 39 minutes 24.42 seconds (2364.42 seconds total)