Starting phenix.real_space_refine on Wed Feb 14 03:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/02_2024/7xow_33361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/02_2024/7xow_33361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/02_2024/7xow_33361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/02_2024/7xow_33361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/02_2024/7xow_33361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xow_33361/02_2024/7xow_33361_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 58 5.16 5 C 5479 2.51 5 N 1468 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 151": "OE1" <-> "OE2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R ARG 333": "NH1" <-> "NH2" Residue "R ARG 396": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" 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: 8566 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2153 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" 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: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "C" 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: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 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: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1798 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 75 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.42, per 1000 atoms: 0.63 Number of scatterers: 8566 At special positions: 0 Unit cell: (112.554, 115.596, 124.722, 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 58 16.00 O 1561 8.00 N 1468 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'R' and resid 55 through 80 Processing helix chain 'R' and resid 88 through 117 removed outlier: 4.165A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Proline residue: R 109 - end of helix Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 123 through 157 Processing helix chain 'R' and resid 159 through 165 removed outlier: 4.291A pdb=" N VAL R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 185 removed outlier: 3.711A pdb=" N ARG R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 215 through 227 Processing helix chain 'R' and resid 229 through 247 Processing helix chain 'R' and resid 326 through 366 removed outlier: 4.413A pdb=" N VAL R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) Proline residue: R 348 - end of helix Proline residue: R 361 - end of helix removed outlier: 3.876A pdb=" N HIS R 364 " --> pdb=" O GLY R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 390 removed outlier: 3.986A pdb=" N SER R 382 " --> pdb=" O LEU R 378 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 396 through 402 removed outlier: 3.533A pdb=" N CYS R 401 " --> pdb=" O ARG R 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.627A pdb=" N THR A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 297 through 308 removed outlier: 4.359A pdb=" N PHE A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 303 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.888A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 115 removed outlier: 6.041A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.994A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.891A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.840A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.916A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.531A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'E' and resid 10 through 12 Processing sheet with id= J, first strand: chain 'E' and resid 92 through 99 removed outlier: 3.642A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.528A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'E' and resid 214 through 219 removed outlier: 6.493A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 266 through 268 removed outlier: 4.193A pdb=" N SER A 219 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 223 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 40 " --> pdb=" O VAL A 200 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1065 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: 2.22 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1467 1.32 - 1.45: 2344 1.45 - 1.57: 4849 1.57 - 1.69: 1 1.69 - 1.82: 85 Bond restraints: 8746 Sorted by residual: bond pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" OH TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.679 1.538 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C TYR R 189 " pdb=" O TYR R 189 " ideal model delta sigma weight residual 1.244 1.202 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" N LEU R 203 " pdb=" CA LEU R 203 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 1.458 1.482 -0.025 1.41e-02 5.03e+03 3.06e+00 ... (remaining 8741 not shown) Histogram of bond angle deviations from ideal: 84.47 - 94.38: 3 94.38 - 104.30: 118 104.30 - 114.21: 5168 114.21 - 124.13: 6381 124.13 - 134.05: 212 Bond angle restraints: 11882 Sorted by residual: angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O2 TYS L 12 " ideal model delta sigma weight residual 114.11 84.47 29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 115.16 88.07 27.09 3.00e+00 1.11e-01 8.16e+01 angle pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" C VAL R 202 " ideal model delta sigma weight residual 110.62 118.97 -8.35 1.02e+00 9.61e-01 6.71e+01 angle pdb=" N GLN R 204 " pdb=" CA GLN R 204 " pdb=" C GLN R 204 " ideal model delta sigma weight residual 111.17 121.67 -10.50 1.41e+00 5.03e-01 5.54e+01 angle pdb=" OH TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 100.21 118.72 -18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 11877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4694 17.60 - 35.19: 391 35.19 - 52.79: 60 52.79 - 70.39: 10 70.39 - 87.98: 4 Dihedral angle restraints: 5159 sinusoidal: 1913 harmonic: 3246 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 dihedral pdb=" C VAL R 202 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" CB VAL R 202 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA LEU A 265 " pdb=" C LEU A 265 " pdb=" N PHE A 266 " pdb=" CA PHE A 266 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1186 0.067 - 0.134: 168 0.134 - 0.201: 10 0.201 - 0.269: 6 0.269 - 0.336: 4 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE L 17 " pdb=" N PHE L 17 " pdb=" C PHE L 17 " pdb=" CB PHE L 17 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA GLN R 204 " pdb=" N GLN R 204 " pdb=" C GLN R 204 " pdb=" CB GLN R 204 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA VAL R 202 " pdb=" N VAL R 202 " pdb=" C VAL R 202 " pdb=" CB VAL R 202 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1371 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 189 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO R 190 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO E 224 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 187 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO R 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 188 " -0.047 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 741 2.74 - 3.28: 8427 3.28 - 3.82: 13484 3.82 - 4.36: 16146 4.36 - 4.90: 29065 Nonbonded interactions: 67863 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.198 2.440 nonbonded pdb=" OD2 ASP B 228 " pdb=" NZ LYS A 209 " model vdw 2.244 2.520 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.250 2.520 nonbonded pdb=" OD1 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.268 2.520 nonbonded pdb=" N CYS A 324 " pdb=" OD2 ASP A 327 " model vdw 2.269 2.520 ... (remaining 67858 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 2.010 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.410 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 0.170 8746 Z= 0.289 Angle : 0.857 29.645 11882 Z= 0.455 Chirality : 0.052 0.336 1374 Planarity : 0.006 0.105 1495 Dihedral : 13.161 87.985 3059 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 1097 helix: -0.41 (0.26), residues: 364 sheet: -1.79 (0.29), residues: 289 loop : -3.05 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.003 0.001 HIS B 54 PHE 0.022 0.002 PHE B 234 TYR 0.013 0.001 TYR R 192 ARG 0.004 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.032 Fit side-chains REVERT: R 73 MET cc_start: 0.7231 (mmt) cc_final: 0.6878 (mmt) REVERT: R 207 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.5572 (m-70) REVERT: R 213 ARG cc_start: 0.6193 (mmt180) cc_final: 0.3788 (ptt-90) REVERT: R 333 ARG cc_start: 0.6314 (ttm170) cc_final: 0.5644 (ttm-80) REVERT: R 398 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6744 (mmp80) REVERT: B 67 SER cc_start: 0.8803 (m) cc_final: 0.8404 (t) REVERT: B 325 MET cc_start: 0.7886 (tpp) cc_final: 0.7674 (tpp) REVERT: E 182 ASN cc_start: 0.8736 (m110) cc_final: 0.8462 (m110) REVERT: A 242 MET cc_start: 0.7403 (tpp) cc_final: 0.6316 (tpp) REVERT: A 305 LYS cc_start: 0.7059 (ttpp) cc_final: 0.6810 (tppt) REVERT: A 339 LYS cc_start: 0.7160 (tttt) cc_final: 0.6951 (tttp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2588 time to fit residues: 57.0810 Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 166 GLN R 196 GLN R 204 GLN B 17 GLN B 35 ASN B 75 GLN B 176 GLN B 220 GLN C 44 HIS E 159 ASN E 167 GLN E 171 GLN A 231 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8746 Z= 0.178 Angle : 0.575 8.503 11882 Z= 0.290 Chirality : 0.043 0.153 1374 Planarity : 0.005 0.084 1495 Dihedral : 4.737 39.781 1219 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 2.13 % Allowed : 9.41 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.68 (0.25), residues: 1097 helix: 0.78 (0.28), residues: 362 sheet: -1.41 (0.29), residues: 291 loop : -2.52 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 253 TYR 0.021 0.001 TYR R 380 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.998 Fit side-chains REVERT: R 207 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.5335 (m-70) REVERT: R 213 ARG cc_start: 0.6161 (mmt180) cc_final: 0.3770 (ptt-90) REVERT: R 333 ARG cc_start: 0.6185 (ttm170) cc_final: 0.5462 (ttm-80) REVERT: R 380 TYR cc_start: 0.7524 (m-80) cc_final: 0.7098 (m-80) REVERT: R 398 ARG cc_start: 0.7029 (mmt90) cc_final: 0.6658 (mmp80) REVERT: B 220 GLN cc_start: 0.7894 (mt0) cc_final: 0.7693 (mt0) REVERT: B 258 ASP cc_start: 0.8580 (t0) cc_final: 0.8018 (t0) REVERT: B 325 MET cc_start: 0.7925 (tpp) cc_final: 0.7486 (tpp) REVERT: E 182 ASN cc_start: 0.8802 (m110) cc_final: 0.8562 (m110) REVERT: A 242 MET cc_start: 0.7495 (tpp) cc_final: 0.6603 (tpp) REVERT: A 339 LYS cc_start: 0.7127 (tttt) cc_final: 0.6911 (tttp) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 0.2131 time to fit residues: 45.3995 Evaluate side-chains 147 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 227 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.0060 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 50.0000 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 166 GLN R 196 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8746 Z= 0.316 Angle : 0.655 9.017 11882 Z= 0.328 Chirality : 0.045 0.180 1374 Planarity : 0.005 0.093 1495 Dihedral : 5.016 43.092 1219 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 3.36 % Allowed : 12.43 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1097 helix: 0.99 (0.28), residues: 363 sheet: -1.35 (0.29), residues: 301 loop : -2.39 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.002 PHE E 27 TYR 0.021 0.002 TYR A 285 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 0.886 Fit side-chains REVERT: R 207 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.5126 (m-70) REVERT: R 213 ARG cc_start: 0.6628 (mmt180) cc_final: 0.4096 (ptt-90) REVERT: R 333 ARG cc_start: 0.6456 (ttm170) cc_final: 0.5744 (ttm-80) REVERT: R 380 TYR cc_start: 0.7599 (m-80) cc_final: 0.7243 (m-80) REVERT: R 398 ARG cc_start: 0.6944 (mmt90) cc_final: 0.6708 (mmp80) REVERT: B 101 MET cc_start: 0.8492 (mtp) cc_final: 0.8229 (mtp) REVERT: B 118 ASP cc_start: 0.7739 (p0) cc_final: 0.7396 (p0) REVERT: B 258 ASP cc_start: 0.8544 (t0) cc_final: 0.8137 (t0) REVERT: B 325 MET cc_start: 0.7972 (tpp) cc_final: 0.7543 (tpp) REVERT: E 116 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7046 (t) REVERT: E 126 ILE cc_start: 0.8094 (mp) cc_final: 0.7815 (mt) REVERT: A 189 ASP cc_start: 0.7971 (t70) cc_final: 0.7751 (t0) REVERT: A 196 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7954 (mtp85) REVERT: A 295 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5198 (m-30) REVERT: A 327 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.6117 (m-30) REVERT: L 15 MET cc_start: 0.6546 (ptp) cc_final: 0.6155 (mtp) outliers start: 30 outliers final: 20 residues processed: 157 average time/residue: 0.2048 time to fit residues: 44.4939 Evaluate side-chains 157 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8746 Z= 0.162 Angle : 0.556 7.850 11882 Z= 0.280 Chirality : 0.042 0.192 1374 Planarity : 0.004 0.079 1495 Dihedral : 4.660 38.688 1219 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.47 % Allowed : 13.89 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 1097 helix: 1.55 (0.28), residues: 355 sheet: -0.95 (0.30), residues: 290 loop : -2.12 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 346 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 253 TYR 0.013 0.001 TYR R 380 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.911 Fit side-chains REVERT: R 184 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7389 (mp) REVERT: R 186 MET cc_start: 0.7167 (mmt) cc_final: 0.6952 (tpp) REVERT: R 204 GLN cc_start: 0.6526 (mt0) cc_final: 0.5710 (pt0) REVERT: R 213 ARG cc_start: 0.6350 (mmt180) cc_final: 0.3797 (ptt-90) REVERT: R 333 ARG cc_start: 0.6245 (ttm170) cc_final: 0.5450 (ttm-80) REVERT: R 380 TYR cc_start: 0.7612 (m-80) cc_final: 0.7332 (m-80) REVERT: R 398 ARG cc_start: 0.6938 (mmt90) cc_final: 0.6623 (mmp80) REVERT: B 101 MET cc_start: 0.8444 (mtp) cc_final: 0.8234 (mtp) REVERT: B 258 ASP cc_start: 0.8342 (t0) cc_final: 0.7912 (t0) REVERT: B 325 MET cc_start: 0.8025 (tpp) cc_final: 0.7638 (tpp) REVERT: E 116 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.7153 (t) REVERT: E 126 ILE cc_start: 0.8114 (mp) cc_final: 0.7856 (mt) REVERT: E 146 SER cc_start: 0.8381 (t) cc_final: 0.8091 (p) REVERT: A 189 ASP cc_start: 0.7894 (t70) cc_final: 0.7600 (t0) REVERT: A 295 ASP cc_start: 0.5980 (OUTLIER) cc_final: 0.5655 (m-30) REVERT: A 327 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.6036 (m-30) REVERT: L 15 MET cc_start: 0.6511 (ptp) cc_final: 0.6164 (mtp) outliers start: 31 outliers final: 15 residues processed: 156 average time/residue: 0.2051 time to fit residues: 44.1264 Evaluate side-chains 147 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 196 GLN R 204 GLN B 75 GLN B 220 GLN B 259 GLN E 82 GLN A 321 HIS A 330 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8746 Z= 0.183 Angle : 0.561 8.052 11882 Z= 0.282 Chirality : 0.042 0.202 1374 Planarity : 0.004 0.079 1495 Dihedral : 4.488 38.276 1217 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.36 % Allowed : 15.79 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.65 (0.26), residues: 1097 helix: 1.71 (0.28), residues: 354 sheet: -0.78 (0.30), residues: 291 loop : -1.95 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 253 TYR 0.014 0.001 TYR A 285 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 0.910 Fit side-chains REVERT: R 184 LEU cc_start: 0.7820 (tt) cc_final: 0.7330 (mp) REVERT: R 196 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.6106 (mp10) REVERT: R 204 GLN cc_start: 0.6558 (mt0) cc_final: 0.5690 (pt0) REVERT: R 213 ARG cc_start: 0.6548 (mmt180) cc_final: 0.4053 (ptt-90) REVERT: R 333 ARG cc_start: 0.6253 (ttm170) cc_final: 0.5496 (ttm-80) REVERT: R 380 TYR cc_start: 0.7632 (m-80) cc_final: 0.7354 (m-80) REVERT: R 398 ARG cc_start: 0.6940 (mmt90) cc_final: 0.6621 (mmp80) REVERT: B 205 ASP cc_start: 0.7837 (p0) cc_final: 0.7632 (p0) REVERT: B 220 GLN cc_start: 0.8027 (mt0) cc_final: 0.7800 (mt0) REVERT: B 258 ASP cc_start: 0.8322 (t0) cc_final: 0.7889 (t0) REVERT: B 325 MET cc_start: 0.8020 (tpp) cc_final: 0.7602 (tpp) REVERT: E 116 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.7196 (t) REVERT: E 146 SER cc_start: 0.8390 (t) cc_final: 0.8112 (p) REVERT: E 180 MET cc_start: 0.7623 (ptm) cc_final: 0.7230 (ptm) REVERT: A 20 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: A 327 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5936 (m-30) outliers start: 30 outliers final: 17 residues processed: 149 average time/residue: 0.2067 time to fit residues: 42.3074 Evaluate side-chains 152 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8746 Z= 0.249 Angle : 0.605 8.429 11882 Z= 0.302 Chirality : 0.044 0.222 1374 Planarity : 0.004 0.082 1495 Dihedral : 4.609 40.369 1217 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.25 % Allowed : 16.80 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1097 helix: 1.70 (0.28), residues: 356 sheet: -0.78 (0.30), residues: 299 loop : -1.90 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE B 253 TYR 0.014 0.001 TYR A 285 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.050 Fit side-chains REVERT: R 196 GLN cc_start: 0.6360 (mp-120) cc_final: 0.5922 (mp10) REVERT: R 204 GLN cc_start: 0.6563 (mt0) cc_final: 0.5634 (pt0) REVERT: R 207 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6377 (m-70) REVERT: R 213 ARG cc_start: 0.6529 (mmt180) cc_final: 0.4074 (ptt-90) REVERT: R 333 ARG cc_start: 0.6338 (ttm170) cc_final: 0.5568 (ttm-80) REVERT: R 380 TYR cc_start: 0.7696 (m-80) cc_final: 0.7436 (m-80) REVERT: R 398 ARG cc_start: 0.6906 (mmt90) cc_final: 0.6656 (mmp80) REVERT: B 205 ASP cc_start: 0.7924 (p0) cc_final: 0.7707 (p0) REVERT: B 258 ASP cc_start: 0.8308 (t0) cc_final: 0.8098 (t0) REVERT: B 325 MET cc_start: 0.8018 (tpp) cc_final: 0.7574 (tpp) REVERT: E 146 SER cc_start: 0.8345 (t) cc_final: 0.8084 (p) REVERT: A 20 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: A 327 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5646 (m-30) outliers start: 29 outliers final: 22 residues processed: 137 average time/residue: 0.2119 time to fit residues: 40.0982 Evaluate side-chains 144 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8746 Z= 0.166 Angle : 0.562 7.720 11882 Z= 0.280 Chirality : 0.042 0.235 1374 Planarity : 0.004 0.076 1495 Dihedral : 4.441 37.697 1217 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.25 % Allowed : 16.57 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.41 (0.26), residues: 1097 helix: 1.86 (0.28), residues: 353 sheet: -0.62 (0.30), residues: 296 loop : -1.80 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 253 TYR 0.008 0.001 TYR R 380 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.164 Fit side-chains REVERT: R 184 LEU cc_start: 0.8000 (tt) cc_final: 0.7462 (mp) REVERT: R 207 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6534 (m-70) REVERT: R 333 ARG cc_start: 0.6209 (ttm170) cc_final: 0.5351 (ttm-80) REVERT: R 398 ARG cc_start: 0.6942 (mmt90) cc_final: 0.6558 (mmp80) REVERT: B 205 ASP cc_start: 0.7889 (p0) cc_final: 0.7679 (p0) REVERT: B 220 GLN cc_start: 0.8039 (mt0) cc_final: 0.7758 (mt0) REVERT: B 325 MET cc_start: 0.8033 (tpp) cc_final: 0.7594 (tpp) REVERT: E 116 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7258 (t) REVERT: E 146 SER cc_start: 0.8384 (t) cc_final: 0.8126 (p) REVERT: E 180 MET cc_start: 0.7517 (ptm) cc_final: 0.7316 (ptm) REVERT: A 20 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: A 196 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7920 (mtp85) REVERT: A 327 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5572 (m-30) outliers start: 29 outliers final: 21 residues processed: 138 average time/residue: 0.2222 time to fit residues: 42.4908 Evaluate side-chains 148 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN R 204 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8746 Z= 0.144 Angle : 0.564 12.599 11882 Z= 0.277 Chirality : 0.042 0.309 1374 Planarity : 0.004 0.075 1495 Dihedral : 4.261 34.966 1217 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.69 % Allowed : 17.25 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.20 (0.26), residues: 1097 helix: 2.04 (0.28), residues: 353 sheet: -0.49 (0.30), residues: 295 loop : -1.69 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 346 HIS 0.003 0.001 HIS A 321 PHE 0.012 0.001 PHE A 49 TYR 0.038 0.001 TYR R 380 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.936 Fit side-chains REVERT: R 333 ARG cc_start: 0.6164 (ttm170) cc_final: 0.5310 (ttm-80) REVERT: R 398 ARG cc_start: 0.6946 (mmt90) cc_final: 0.6572 (mmp80) REVERT: B 220 GLN cc_start: 0.7975 (mt0) cc_final: 0.7652 (mt0) REVERT: B 325 MET cc_start: 0.8048 (tpp) cc_final: 0.7697 (tpp) REVERT: E 116 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7271 (t) REVERT: E 146 SER cc_start: 0.8401 (t) cc_final: 0.8147 (p) REVERT: A 20 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: A 46 LYS cc_start: 0.7273 (pttt) cc_final: 0.6938 (ttpt) REVERT: A 327 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.5566 (m-30) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.2124 time to fit residues: 41.2589 Evaluate side-chains 137 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8746 Z= 0.178 Angle : 0.573 9.148 11882 Z= 0.291 Chirality : 0.043 0.285 1374 Planarity : 0.004 0.077 1495 Dihedral : 4.303 35.809 1217 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.91 % Allowed : 17.36 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.16 (0.26), residues: 1097 helix: 2.06 (0.28), residues: 355 sheet: -0.41 (0.30), residues: 294 loop : -1.71 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 346 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE B 253 TYR 0.008 0.001 TYR R 189 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.055 Fit side-chains REVERT: R 333 ARG cc_start: 0.6212 (ttm170) cc_final: 0.5349 (ttm-80) REVERT: R 398 ARG cc_start: 0.7122 (mmt90) cc_final: 0.6768 (mmp80) REVERT: B 156 GLN cc_start: 0.8125 (mt0) cc_final: 0.7875 (mt0) REVERT: B 325 MET cc_start: 0.8048 (tpp) cc_final: 0.7671 (tpp) REVERT: E 116 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7259 (t) REVERT: E 146 SER cc_start: 0.8396 (t) cc_final: 0.8171 (p) REVERT: A 20 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: A 269 LYS cc_start: 0.8429 (mttp) cc_final: 0.8202 (mtpt) REVERT: A 327 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5656 (m-30) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.2297 time to fit residues: 42.0762 Evaluate side-chains 141 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8746 Z= 0.173 Angle : 0.580 9.967 11882 Z= 0.290 Chirality : 0.043 0.240 1374 Planarity : 0.004 0.077 1495 Dihedral : 4.282 32.904 1217 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.80 % Allowed : 17.36 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.12 (0.26), residues: 1097 helix: 2.10 (0.28), residues: 355 sheet: -0.38 (0.30), residues: 292 loop : -1.68 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 346 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 49 TYR 0.008 0.001 TYR R 189 ARG 0.008 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.959 Fit side-chains REVERT: R 333 ARG cc_start: 0.6204 (ttm170) cc_final: 0.5340 (ttm-80) REVERT: R 398 ARG cc_start: 0.7117 (mmt90) cc_final: 0.6773 (mmp80) REVERT: B 156 GLN cc_start: 0.8116 (mt0) cc_final: 0.7851 (mt0) REVERT: B 325 MET cc_start: 0.8052 (tpp) cc_final: 0.7583 (tpp) REVERT: E 116 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7241 (t) REVERT: E 146 SER cc_start: 0.8401 (t) cc_final: 0.8183 (p) REVERT: A 20 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: A 269 LYS cc_start: 0.8463 (mttp) cc_final: 0.8259 (mtpt) REVERT: A 327 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5597 (m-30) outliers start: 25 outliers final: 20 residues processed: 133 average time/residue: 0.2174 time to fit residues: 39.7232 Evaluate side-chains 140 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144673 restraints weight = 9081.617| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.88 r_work: 0.3615 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8746 Z= 0.214 Angle : 0.595 8.428 11882 Z= 0.297 Chirality : 0.043 0.235 1374 Planarity : 0.004 0.080 1495 Dihedral : 4.393 34.783 1217 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.02 % Allowed : 16.80 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.12 (0.26), residues: 1097 helix: 2.08 (0.28), residues: 355 sheet: -0.47 (0.30), residues: 297 loop : -1.63 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 346 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE B 253 TYR 0.009 0.001 TYR E 178 ARG 0.006 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.84 seconds wall clock time: 38 minutes 8.37 seconds (2288.37 seconds total)