Starting phenix.real_space_refine on Mon Mar 11 14:51:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/03_2024/7yjn_33875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/03_2024/7yjn_33875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/03_2024/7yjn_33875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/03_2024/7yjn_33875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/03_2024/7yjn_33875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/03_2024/7yjn_33875_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.101 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 5476 2.51 5 N 1445 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8528 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3230 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "B" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3592 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1122 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 186 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 383 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.92, per 1000 atoms: 0.58 Number of scatterers: 8528 At special positions: 0 Unit cell: (89.64, 82.08, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 1557 8.00 N 1445 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 5 sheets defined 45.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.857A pdb=" N ASP A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 72' Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 178 through 189 removed outlier: 4.318A pdb=" N MET A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.552A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'B' and resid 6 through 35 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 170 through 181 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 196 through 203 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 259 through 268 Processing helix chain 'B' and resid 291 through 294 No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.682A pdb=" N GLN B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 409 through 420 removed outlier: 3.553A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'D' and resid 26 through 44 removed outlier: 3.791A pdb=" N MET D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 70 Processing helix chain 'D' and resid 88 through 95 removed outlier: 6.443A pdb=" N ASP D 93 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Proline residue: D 109 - end of helix removed outlier: 4.035A pdb=" N THR D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'E' and resid 37 through 53 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 22 through 46 removed outlier: 3.845A pdb=" N VAL C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 33 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.667A pdb=" N ARG A 277 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA A 251 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 279 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 309 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 390 through 392 Processing sheet with id= C, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.636A pdb=" N ALA B 163 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 275 " --> pdb=" O MET B 306 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.481A pdb=" N TYR B 272 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.501A pdb=" N MET B 401 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1044 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: 2.07 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1363 1.27 - 1.40: 2196 1.40 - 1.54: 5003 1.54 - 1.67: 80 1.67 - 1.81: 76 Bond restraints: 8718 Sorted by residual: bond pdb=" CA THR D 64 " pdb=" C THR D 64 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.37e-02 5.33e+03 8.46e+01 bond pdb=" C LEU B 103 " pdb=" N ASN B 104 " ideal model delta sigma weight residual 1.331 1.203 0.129 1.40e-02 5.10e+03 8.43e+01 bond pdb=" C LEU B 103 " pdb=" O LEU B 103 " ideal model delta sigma weight residual 1.234 1.130 0.105 1.15e-02 7.56e+03 8.31e+01 bond pdb=" CA LEU B 103 " pdb=" C LEU B 103 " ideal model delta sigma weight residual 1.520 1.414 0.107 1.20e-02 6.94e+03 7.89e+01 bond pdb=" C CYS B 102 " pdb=" O CYS B 102 " ideal model delta sigma weight residual 1.235 1.133 0.103 1.26e-02 6.30e+03 6.64e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 95.02 - 102.85: 99 102.85 - 110.67: 2952 110.67 - 118.50: 3945 118.50 - 126.33: 4683 126.33 - 134.16: 137 Bond angle restraints: 11816 Sorted by residual: angle pdb=" N PHE A 189 " pdb=" CA PHE A 189 " pdb=" C PHE A 189 " ideal model delta sigma weight residual 113.16 130.33 -17.17 1.24e+00 6.50e-01 1.92e+02 angle pdb=" C ILE C 8 " pdb=" CA ILE C 8 " pdb=" CB ILE C 8 " ideal model delta sigma weight residual 111.97 98.11 13.86 1.28e+00 6.10e-01 1.17e+02 angle pdb=" C MET D 71 " pdb=" N LYS D 72 " pdb=" CA LYS D 72 " ideal model delta sigma weight residual 122.19 109.66 12.53 1.41e+00 5.03e-01 7.90e+01 angle pdb=" C PHE D 142 " pdb=" N PRO D 143 " pdb=" CA PRO D 143 " ideal model delta sigma weight residual 119.84 130.64 -10.80 1.25e+00 6.40e-01 7.46e+01 angle pdb=" C VAL B 223 " pdb=" CA VAL B 223 " pdb=" CB VAL B 223 " ideal model delta sigma weight residual 112.14 101.03 11.11 1.35e+00 5.49e-01 6.77e+01 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4540 17.95 - 35.89: 499 35.89 - 53.83: 132 53.83 - 71.78: 17 71.78 - 89.72: 4 Dihedral angle restraints: 5192 sinusoidal: 2029 harmonic: 3163 Sorted by residual: dihedral pdb=" C PHE A 183 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual -122.60 -151.10 28.50 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual 122.80 150.73 -27.93 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual 122.80 143.93 -21.13 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1272 0.261 - 0.522: 51 0.522 - 0.782: 14 0.782 - 1.043: 0 1.043 - 1.304: 2 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CA PHE A 183 " pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CB PHE A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" CA LEU B 259 " pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CB LEU B 259 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CG LEU D 129 " pdb=" CB LEU D 129 " pdb=" CD1 LEU D 129 " pdb=" CD2 LEU D 129 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 1336 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 186 " -0.145 5.00e-02 4.00e+02 2.18e-01 7.59e+01 pdb=" N PRO A 187 " 0.377 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 68 " -0.026 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C PHE D 68 " 0.087 2.00e-02 2.50e+03 pdb=" O PHE D 68 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS D 69 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 229 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ALA B 229 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA B 229 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU B 230 " -0.028 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 45 2.40 - 3.03: 5840 3.03 - 3.65: 12216 3.65 - 4.28: 17504 4.28 - 4.90: 30645 Nonbonded interactions: 66250 Sorted by model distance: nonbonded pdb=" O GLY B 314 " pdb=" OE1 GLN B 350 " model vdw 1.776 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NH2 ARG B 58 " model vdw 1.869 2.520 nonbonded pdb=" OE1 GLN B 24 " pdb=" CE2 PHE B 54 " model vdw 1.908 3.340 nonbonded pdb=" O ALA B 229 " pdb=" N GLY B 231 " model vdw 1.910 2.520 nonbonded pdb=" O THR D 28 " pdb=" C THR D 29 " model vdw 1.946 3.270 ... (remaining 66245 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.040 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.520 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.019 0.149 8718 Z= 1.229 Angle : 1.743 21.282 11816 Z= 1.050 Chirality : 0.133 1.304 1339 Planarity : 0.011 0.218 1486 Dihedral : 15.887 89.725 3162 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 1.94 % Allowed : 11.10 % Favored : 86.96 % Rotamer: Outliers : 8.37 % Allowed : 7.28 % Favored : 84.35 % Cbeta Deviations : 2.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.25), residues: 1081 helix: -0.36 (0.22), residues: 543 sheet: -3.45 (0.48), residues: 80 loop : -2.75 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP D 70 HIS 0.019 0.003 HIS B 61 PHE 0.042 0.004 PHE B 20 TYR 0.029 0.003 TYR B 406 ARG 0.010 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 126 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6702 (mmt) REVERT: A 368 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (t0) REVERT: A 388 LYS cc_start: 0.7788 (mttp) cc_final: 0.6983 (tttp) REVERT: A 473 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: B 28 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 90 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6954 (t0) REVERT: B 94 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: B 113 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 222 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7122 (ttm170) REVERT: D 24 PRO cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (Cg_endo) REVERT: D 30 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 72 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8778 (mttt) REVERT: D 113 TYR cc_start: 0.8295 (t80) cc_final: 0.6948 (t80) REVERT: D 122 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: D 128 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 2 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6230 (p0) outliers start: 77 outliers final: 39 residues processed: 191 average time/residue: 0.2290 time to fit residues: 58.4292 Evaluate side-chains 157 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 105 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 24 PRO Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 61 HIS B 227 GLN B 279 HIS D 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8718 Z= 0.220 Angle : 0.716 9.804 11816 Z= 0.371 Chirality : 0.046 0.187 1339 Planarity : 0.006 0.059 1486 Dihedral : 9.384 59.877 1296 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Rotamer: Outliers : 4.67 % Allowed : 14.13 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1081 helix: 0.83 (0.23), residues: 542 sheet: -2.92 (0.49), residues: 85 loop : -2.51 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 239 HIS 0.008 0.001 HIS D 124 PHE 0.040 0.002 PHE A 183 TYR 0.019 0.002 TYR B 85 ARG 0.005 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7245 (t-170) REVERT: A 388 LYS cc_start: 0.7783 (mttp) cc_final: 0.6994 (tttp) REVERT: A 473 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: B 107 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (p) REVERT: B 113 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: B 276 ASP cc_start: 0.7526 (t70) cc_final: 0.6787 (t70) REVERT: B 417 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 30 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7557 (t80) REVERT: D 70 TRP cc_start: 0.7644 (t60) cc_final: 0.7393 (t60) REVERT: D 92 MET cc_start: 0.7942 (mmm) cc_final: 0.7370 (tpp) REVERT: D 113 TYR cc_start: 0.8150 (t80) cc_final: 0.6882 (t80) REVERT: D 142 PHE cc_start: 0.8093 (m-80) cc_final: 0.7684 (m-80) REVERT: C 5 GLN cc_start: 0.8145 (tp40) cc_final: 0.7868 (tt0) outliers start: 43 outliers final: 22 residues processed: 156 average time/residue: 0.2195 time to fit residues: 46.5431 Evaluate side-chains 142 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 36 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 375 GLN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8718 Z= 0.305 Angle : 0.680 7.631 11816 Z= 0.354 Chirality : 0.046 0.202 1339 Planarity : 0.005 0.057 1486 Dihedral : 7.687 57.520 1231 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.97 % Favored : 90.75 % Rotamer: Outliers : 3.91 % Allowed : 16.52 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1081 helix: 1.22 (0.23), residues: 544 sheet: -2.96 (0.51), residues: 80 loop : -2.38 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 239 HIS 0.004 0.001 HIS D 124 PHE 0.035 0.002 PHE A 183 TYR 0.020 0.002 TYR B 85 ARG 0.004 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7452 (t-170) REVERT: B 107 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8564 (p) REVERT: B 417 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 30 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7467 (t80) REVERT: D 70 TRP cc_start: 0.7762 (t60) cc_final: 0.7504 (t60) outliers start: 36 outliers final: 22 residues processed: 145 average time/residue: 0.2007 time to fit residues: 40.3985 Evaluate side-chains 135 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0000 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 365 GLN A 375 GLN B 214 HIS B 407 ASN D 84 ASN D 144 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8718 Z= 0.171 Angle : 0.589 9.061 11816 Z= 0.303 Chirality : 0.042 0.180 1339 Planarity : 0.005 0.059 1486 Dihedral : 6.613 58.231 1216 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.80 % Allowed : 18.48 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 1081 helix: 1.57 (0.23), residues: 551 sheet: -2.22 (0.49), residues: 105 loop : -2.29 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 239 HIS 0.003 0.001 HIS D 124 PHE 0.027 0.001 PHE A 183 TYR 0.018 0.001 TYR B 85 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7485 (t-170) REVERT: A 182 MET cc_start: 0.7573 (mmm) cc_final: 0.7162 (mmt) REVERT: A 348 LEU cc_start: 0.8749 (mt) cc_final: 0.8426 (tp) REVERT: A 413 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7647 (tmtt) REVERT: B 417 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7633 (mm-30) REVERT: D 30 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7676 (t80) REVERT: D 70 TRP cc_start: 0.7692 (t60) cc_final: 0.7398 (t60) outliers start: 35 outliers final: 24 residues processed: 145 average time/residue: 0.2137 time to fit residues: 42.3040 Evaluate side-chains 139 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 76 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 375 GLN D 84 ASN D 94 ASN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8718 Z= 0.147 Angle : 0.566 8.866 11816 Z= 0.293 Chirality : 0.042 0.218 1339 Planarity : 0.004 0.053 1486 Dihedral : 6.130 59.246 1212 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 4.24 % Allowed : 19.35 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 1081 helix: 1.62 (0.23), residues: 559 sheet: -1.96 (0.51), residues: 105 loop : -2.11 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 239 HIS 0.003 0.001 HIS B 214 PHE 0.028 0.001 PHE A 183 TYR 0.019 0.001 TYR B 85 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7384 (t-170) REVERT: A 348 LEU cc_start: 0.8758 (mt) cc_final: 0.8475 (tp) REVERT: A 413 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7633 (tmtt) REVERT: B 417 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7578 (mm-30) REVERT: D 30 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7756 (t80) REVERT: D 70 TRP cc_start: 0.7593 (t60) cc_final: 0.7310 (t60) REVERT: C 19 MET cc_start: 0.8844 (ptp) cc_final: 0.8582 (mtm) outliers start: 39 outliers final: 23 residues processed: 157 average time/residue: 0.2027 time to fit residues: 44.0186 Evaluate side-chains 142 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN D 84 ASN D 94 ASN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8718 Z= 0.164 Angle : 0.572 9.133 11816 Z= 0.292 Chirality : 0.042 0.148 1339 Planarity : 0.004 0.052 1486 Dihedral : 5.909 59.073 1210 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.29 % Favored : 93.52 % Rotamer: Outliers : 4.46 % Allowed : 19.78 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1081 helix: 1.62 (0.23), residues: 559 sheet: -1.85 (0.51), residues: 105 loop : -2.00 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 126 HIS 0.003 0.001 HIS B 214 PHE 0.029 0.001 PHE A 183 TYR 0.018 0.001 TYR B 85 ARG 0.004 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: A 125 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7425 (t-170) REVERT: A 136 LEU cc_start: 0.8485 (tp) cc_final: 0.8254 (mt) REVERT: A 348 LEU cc_start: 0.8754 (mt) cc_final: 0.8512 (tp) REVERT: A 473 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7555 (ttp80) REVERT: B 29 PHE cc_start: 0.7134 (t80) cc_final: 0.6760 (m-80) REVERT: D 30 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7783 (t80) REVERT: D 70 TRP cc_start: 0.7617 (t60) cc_final: 0.7298 (t60) REVERT: D 97 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7266 (mm-40) REVERT: C 19 MET cc_start: 0.8833 (ptp) cc_final: 0.8591 (mtm) outliers start: 41 outliers final: 28 residues processed: 148 average time/residue: 0.2141 time to fit residues: 43.1680 Evaluate side-chains 143 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 47 optimal weight: 0.0060 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 375 GLN D 84 ASN D 94 ASN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8718 Z= 0.151 Angle : 0.575 11.043 11816 Z= 0.289 Chirality : 0.041 0.154 1339 Planarity : 0.004 0.052 1486 Dihedral : 5.557 56.619 1207 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.83 % Favored : 93.99 % Rotamer: Outliers : 3.80 % Allowed : 20.54 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1081 helix: 1.66 (0.23), residues: 563 sheet: -1.80 (0.51), residues: 105 loop : -1.94 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 239 HIS 0.003 0.001 HIS B 214 PHE 0.031 0.001 PHE A 183 TYR 0.016 0.001 TYR B 85 ARG 0.003 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6522 (pm20) REVERT: A 125 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7443 (t-170) REVERT: A 136 LEU cc_start: 0.8462 (tp) cc_final: 0.8229 (mt) REVERT: A 348 LEU cc_start: 0.8667 (mt) cc_final: 0.8460 (tp) REVERT: A 413 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7589 (tmtt) REVERT: A 473 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7718 (ttm170) REVERT: B 29 PHE cc_start: 0.7046 (t80) cc_final: 0.6742 (m-80) REVERT: B 299 THR cc_start: 0.8220 (p) cc_final: 0.7896 (p) REVERT: B 417 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7830 (mm-30) REVERT: D 30 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7697 (t80) REVERT: D 70 TRP cc_start: 0.7511 (t60) cc_final: 0.7191 (t60) outliers start: 35 outliers final: 29 residues processed: 146 average time/residue: 0.2260 time to fit residues: 45.0418 Evaluate side-chains 147 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN B 24 GLN D 84 ASN D 94 ASN D 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8718 Z= 0.200 Angle : 0.602 12.153 11816 Z= 0.303 Chirality : 0.042 0.148 1339 Planarity : 0.004 0.049 1486 Dihedral : 5.607 53.508 1207 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.51 % Rotamer: Outliers : 3.80 % Allowed : 20.33 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1081 helix: 1.66 (0.23), residues: 562 sheet: -1.79 (0.51), residues: 105 loop : -1.94 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.031 0.001 PHE A 183 TYR 0.017 0.001 TYR B 85 ARG 0.004 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: A 125 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7565 (t-170) REVERT: A 136 LEU cc_start: 0.8453 (tp) cc_final: 0.8229 (mt) REVERT: A 348 LEU cc_start: 0.8735 (mt) cc_final: 0.8462 (tp) REVERT: A 413 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7633 (tmtt) REVERT: A 473 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7582 (ttp80) REVERT: A 477 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7618 (tt0) REVERT: B 299 THR cc_start: 0.8335 (p) cc_final: 0.7995 (p) REVERT: B 417 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7857 (mm-30) REVERT: D 70 TRP cc_start: 0.7555 (t60) cc_final: 0.7206 (t60) outliers start: 35 outliers final: 27 residues processed: 140 average time/residue: 0.2170 time to fit residues: 41.4748 Evaluate side-chains 138 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 144 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8718 Z= 0.159 Angle : 0.579 10.974 11816 Z= 0.291 Chirality : 0.041 0.158 1339 Planarity : 0.004 0.051 1486 Dihedral : 5.400 51.615 1205 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.92 % Favored : 93.89 % Rotamer: Outliers : 3.59 % Allowed : 20.11 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 1081 helix: 1.75 (0.23), residues: 557 sheet: -1.73 (0.51), residues: 106 loop : -1.77 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 126 HIS 0.004 0.001 HIS B 214 PHE 0.031 0.001 PHE A 183 TYR 0.016 0.001 TYR B 85 ARG 0.004 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6458 (pm20) REVERT: A 125 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7505 (t-170) REVERT: A 136 LEU cc_start: 0.8456 (tp) cc_final: 0.8233 (mt) REVERT: A 348 LEU cc_start: 0.8689 (mt) cc_final: 0.8431 (tp) REVERT: A 413 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7595 (tmtt) REVERT: A 473 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7571 (ttp80) REVERT: A 477 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7591 (tt0) REVERT: B 299 THR cc_start: 0.8343 (p) cc_final: 0.7990 (p) REVERT: B 417 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 30 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7888 (t80) outliers start: 33 outliers final: 27 residues processed: 141 average time/residue: 0.2143 time to fit residues: 41.5277 Evaluate side-chains 140 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8718 Z= 0.182 Angle : 0.588 10.712 11816 Z= 0.297 Chirality : 0.042 0.158 1339 Planarity : 0.004 0.050 1486 Dihedral : 5.405 52.597 1205 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 3.70 % Allowed : 19.78 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 1081 helix: 1.73 (0.23), residues: 560 sheet: -1.65 (0.52), residues: 106 loop : -1.75 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.033 0.001 PHE A 183 TYR 0.016 0.001 TYR B 85 ARG 0.004 0.000 ARG E 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: A 125 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7593 (t-170) REVERT: A 136 LEU cc_start: 0.8474 (tp) cc_final: 0.8237 (mt) REVERT: A 348 LEU cc_start: 0.8761 (mt) cc_final: 0.8455 (tp) REVERT: A 473 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7496 (ttm170) REVERT: A 477 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7432 (tt0) REVERT: B 299 THR cc_start: 0.8375 (p) cc_final: 0.8055 (p) REVERT: B 417 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7821 (mm-30) REVERT: D 30 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7907 (t80) REVERT: D 97 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7500 (mt0) outliers start: 34 outliers final: 27 residues processed: 137 average time/residue: 0.2094 time to fit residues: 39.4782 Evaluate side-chains 139 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123626 restraints weight = 12339.428| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.3364 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8718 Z= 0.162 Angle : 0.585 10.503 11816 Z= 0.294 Chirality : 0.042 0.162 1339 Planarity : 0.004 0.051 1486 Dihedral : 5.175 53.013 1203 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 3.48 % Allowed : 20.33 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1081 helix: 1.77 (0.23), residues: 558 sheet: -1.58 (0.52), residues: 106 loop : -1.68 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.033 0.001 PHE A 183 TYR 0.015 0.001 TYR B 85 ARG 0.004 0.000 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.14 seconds wall clock time: 38 minutes 1.50 seconds (2281.50 seconds total)