Starting phenix.real_space_refine on Sat Aug 3 13:19:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/08_2024/7f58_31461.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/08_2024/7f58_31461.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/7f58_31461/08_2024/7f58_31461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/08_2024/7f58_31461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/08_2024/7f58_31461.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/08_2024/7f58_31461.cif" } 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 Cl 1 4.86 5 C 5112 2.51 5 N 1389 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 42": "OE1" <-> "OE2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 315": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8065 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 49 Unusual residues: {' CA': 1, '1I8': 1} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.59 Number of scatterers: 8065 At special positions: 0 Unit cell: (86.19, 96.33, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 62 16.00 O 1500 8.00 N 1389 7.00 C 5112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.5 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 44.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.974A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 removed outlier: 4.007A pdb=" N THR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 153 removed outlier: 4.051A pdb=" N ASN R 123 " --> pdb=" O VAL R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 190 through 228 removed outlier: 3.586A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET R 200 " --> pdb=" O CYS R 196 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.813A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 Processing helix chain 'R' and resid 283 through 302 removed outlier: 3.528A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 306 through 320 Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.943A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.696A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.978A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.705A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.447A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.877A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.247A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.129A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.573A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.907A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.537A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.651A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.283A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.508A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.739A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.503A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1245 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: 2.15 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1313 1.31 - 1.44: 2213 1.44 - 1.57: 4594 1.57 - 1.70: 5 1.70 - 1.82: 88 Bond restraints: 8213 Sorted by residual: bond pdb=" C33 1I8 R 601 " pdb=" C38 1I8 R 601 " ideal model delta sigma weight residual 1.388 1.572 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C28 1I8 R 601 " pdb=" N07 1I8 R 601 " ideal model delta sigma weight residual 1.337 1.512 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C35 1I8 R 601 " pdb=" C39 1I8 R 601 " ideal model delta sigma weight residual 1.387 1.562 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" C39 1I8 R 601 " pdb=" C42 1I8 R 601 " ideal model delta sigma weight residual 1.390 1.564 -0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C31 1I8 R 601 " pdb=" C36 1I8 R 601 " ideal model delta sigma weight residual 1.386 1.549 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 8208 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 134 105.89 - 112.92: 4424 112.92 - 119.95: 2792 119.95 - 126.98: 3686 126.98 - 134.02: 84 Bond angle restraints: 11120 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 111.28 121.24 -9.96 1.09e+00 8.42e-01 8.34e+01 angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.13 116.75 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" N VAL B 315 " pdb=" CA VAL B 315 " pdb=" C VAL B 315 " ideal model delta sigma weight residual 106.21 111.01 -4.80 1.07e+00 8.73e-01 2.01e+01 angle pdb=" CA PRO R 299 " pdb=" N PRO R 299 " pdb=" CD PRO R 299 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.92e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 118.74 -5.21 1.39e+00 5.18e-01 1.41e+01 ... (remaining 11115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 4691 21.97 - 43.94: 199 43.94 - 65.92: 44 65.92 - 87.89: 9 87.89 - 109.86: 3 Dihedral angle restraints: 4946 sinusoidal: 1974 harmonic: 2972 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -13.19 -72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -40.19 -45.81 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" N07 1I8 R 601 " pdb=" C28 1I8 R 601 " pdb=" C29 1I8 R 601 " pdb=" N09 1I8 R 601 " ideal model delta sinusoidal sigma weight residual -1.56 108.30 -109.86 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1008 0.056 - 0.112: 219 0.112 - 0.168: 37 0.168 - 0.225: 5 0.225 - 0.281: 2 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CB ILE R 194 " pdb=" CA ILE R 194 " pdb=" CG1 ILE R 194 " pdb=" CG2 ILE R 194 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA SER B 316 " pdb=" N SER B 316 " pdb=" C SER B 316 " pdb=" CB SER B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1268 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 298 " -0.096 5.00e-02 4.00e+02 1.43e-01 3.28e+01 pdb=" N PRO R 299 " 0.248 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 374 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ARG A 374 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG A 374 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 375 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 126 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C ASP R 126 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP R 126 " 0.019 2.00e-02 2.50e+03 pdb=" N SER R 127 " 0.017 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2161 2.80 - 3.33: 7736 3.33 - 3.85: 13691 3.85 - 4.38: 16483 4.38 - 4.90: 28030 Nonbonded interactions: 68101 Sorted by model distance: nonbonded pdb=" NH1 ARG R 305 " pdb=" OE2 GLU A 392 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.299 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.301 3.120 nonbonded pdb=" OE1 GLN A 236 " pdb=" NH1 ARG B 314 " model vdw 2.310 3.120 ... (remaining 68096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.460 Process input model: 23.940 Find NCS groups from input model: 0.070 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.008 0.184 8213 Z= 0.524 Angle : 0.790 9.956 11120 Z= 0.467 Chirality : 0.049 0.281 1271 Planarity : 0.006 0.143 1410 Dihedral : 13.303 109.858 3008 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 0.23 % Allowed : 4.09 % Favored : 95.68 % 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: 0.89 (0.26), residues: 1001 helix: 0.84 (0.24), residues: 405 sheet: 0.88 (0.36), residues: 211 loop : 0.35 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 262 TYR 0.020 0.002 TYR A 339 ARG 0.008 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: R 215 MET cc_start: 0.8368 (mtp) cc_final: 0.8129 (mtm) REVERT: R 220 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6754 (ttp-170) REVERT: R 309 LEU cc_start: 0.7564 (mt) cc_final: 0.7269 (tt) REVERT: B 61 MET cc_start: 0.7152 (tmm) cc_final: 0.6904 (ttp) REVERT: B 186 ASP cc_start: 0.7380 (m-30) cc_final: 0.7040 (m-30) REVERT: B 325 MET cc_start: 0.7518 (mmm) cc_final: 0.7179 (mmt) REVERT: N 108 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5738 (m-80) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.2450 time to fit residues: 65.2660 Evaluate side-chains 157 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 ASN R 294 ASN A 357 HIS B 9 GLN B 16 ASN B 32 GLN B 132 ASN B 176 GLN B 259 GLN N 3 GLN N 13 GLN N 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.003 0.025 8213 Z= 0.198 Angle : 0.551 7.398 11120 Z= 0.301 Chirality : 0.043 0.156 1271 Planarity : 0.005 0.082 1410 Dihedral : 7.140 103.380 1161 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.48 % Allowed : 8.18 % Favored : 90.34 % 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: 1.67 (0.26), residues: 1001 helix: 2.01 (0.24), residues: 410 sheet: 0.76 (0.34), residues: 221 loop : 0.44 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE N 68 TYR 0.017 0.001 TYR A 339 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8151 (ttm) cc_final: 0.7804 (ttp) REVERT: A 343 ASP cc_start: 0.7783 (m-30) cc_final: 0.7481 (m-30) REVERT: B 97 SER cc_start: 0.8287 (p) cc_final: 0.7882 (m) REVERT: B 186 ASP cc_start: 0.7308 (m-30) cc_final: 0.7072 (m-30) REVERT: B 254 ASP cc_start: 0.7812 (p0) cc_final: 0.7444 (t0) REVERT: G 47 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7142 (mt-10) outliers start: 13 outliers final: 7 residues processed: 173 average time/residue: 0.2158 time to fit residues: 49.4904 Evaluate side-chains 156 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 0.1980 overall best weight: 0.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8213 Z= 0.145 Angle : 0.484 7.120 11120 Z= 0.264 Chirality : 0.041 0.160 1271 Planarity : 0.004 0.064 1410 Dihedral : 6.692 100.160 1159 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 9.20 % Favored : 89.09 % 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: 1.91 (0.26), residues: 1001 helix: 2.34 (0.24), residues: 410 sheet: 0.79 (0.33), residues: 228 loop : 0.43 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE R 262 TYR 0.013 0.001 TYR A 339 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7686 (m-30) cc_final: 0.7396 (m-30) REVERT: B 97 SER cc_start: 0.8235 (p) cc_final: 0.7902 (m) REVERT: B 254 ASP cc_start: 0.7799 (p0) cc_final: 0.7429 (t0) outliers start: 15 outliers final: 11 residues processed: 166 average time/residue: 0.2057 time to fit residues: 45.7600 Evaluate side-chains 156 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 74 ASN A 31 GLN B 32 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8213 Z= 0.381 Angle : 0.611 6.866 11120 Z= 0.329 Chirality : 0.045 0.206 1271 Planarity : 0.005 0.056 1410 Dihedral : 7.077 98.367 1159 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.07 % Allowed : 10.11 % Favored : 86.82 % 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: 1.33 (0.26), residues: 1001 helix: 1.91 (0.24), residues: 413 sheet: 0.39 (0.33), residues: 232 loop : 0.13 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 99 HIS 0.011 0.002 HIS A 357 PHE 0.032 0.003 PHE N 108 TYR 0.027 0.002 TYR A 339 ARG 0.006 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 200 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6147 (ptp) REVERT: R 281 MET cc_start: 0.8873 (mmt) cc_final: 0.7993 (mmt) REVERT: A 20 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6973 (mtm110) REVERT: A 343 ASP cc_start: 0.7812 (m-30) cc_final: 0.7499 (m-30) REVERT: B 186 ASP cc_start: 0.7521 (m-30) cc_final: 0.7165 (m-30) REVERT: B 188 MET cc_start: 0.8658 (mmm) cc_final: 0.8384 (mmm) REVERT: G 47 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7347 (mt-10) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.2336 time to fit residues: 50.0787 Evaluate side-chains 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 200 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 371 ASN B 32 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8213 Z= 0.168 Angle : 0.487 7.193 11120 Z= 0.265 Chirality : 0.041 0.171 1271 Planarity : 0.004 0.053 1410 Dihedral : 6.705 96.863 1159 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.39 % Allowed : 12.84 % Favored : 84.77 % 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: 1.54 (0.27), residues: 1001 helix: 2.20 (0.24), residues: 415 sheet: 0.32 (0.33), residues: 236 loop : 0.19 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5564 (mm) REVERT: R 281 MET cc_start: 0.8843 (mmt) cc_final: 0.7894 (mmt) REVERT: A 343 ASP cc_start: 0.7667 (m-30) cc_final: 0.7392 (m-30) REVERT: B 226 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 254 ASP cc_start: 0.7776 (p0) cc_final: 0.7421 (t0) REVERT: G 47 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7333 (mt-10) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 0.2436 time to fit residues: 52.4605 Evaluate side-chains 155 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8213 Z= 0.168 Angle : 0.478 6.788 11120 Z= 0.260 Chirality : 0.041 0.159 1271 Planarity : 0.004 0.051 1410 Dihedral : 6.536 94.106 1159 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.30 % Allowed : 13.18 % Favored : 83.52 % 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: 1.59 (0.27), residues: 1001 helix: 2.25 (0.25), residues: 419 sheet: 0.32 (0.33), residues: 236 loop : 0.21 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 280 TYR 0.013 0.001 TYR A 339 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5318 (mm) REVERT: R 161 MET cc_start: 0.6477 (mmt) cc_final: 0.6179 (tpp) REVERT: R 281 MET cc_start: 0.8813 (mmt) cc_final: 0.7834 (mmt) REVERT: A 343 ASP cc_start: 0.7689 (m-30) cc_final: 0.7417 (m-30) REVERT: B 226 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 254 ASP cc_start: 0.7773 (p0) cc_final: 0.7396 (t0) REVERT: G 47 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7256 (mt-10) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 0.2245 time to fit residues: 50.5196 Evaluate side-chains 161 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8213 Z= 0.140 Angle : 0.464 6.103 11120 Z= 0.253 Chirality : 0.040 0.144 1271 Planarity : 0.004 0.049 1410 Dihedral : 6.356 90.287 1159 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.93 % Allowed : 14.32 % Favored : 83.75 % 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: 1.66 (0.27), residues: 1001 helix: 2.31 (0.25), residues: 422 sheet: 0.27 (0.33), residues: 235 loop : 0.29 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR A 339 ARG 0.007 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5203 (mm) REVERT: R 161 MET cc_start: 0.6477 (mmt) cc_final: 0.6182 (tpp) REVERT: R 281 MET cc_start: 0.8806 (mmt) cc_final: 0.7934 (mmt) REVERT: B 175 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7625 (tt0) REVERT: B 226 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 254 ASP cc_start: 0.7776 (p0) cc_final: 0.7385 (t0) REVERT: G 47 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7216 (mt-10) outliers start: 17 outliers final: 12 residues processed: 162 average time/residue: 0.2147 time to fit residues: 46.2465 Evaluate side-chains 154 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8213 Z= 0.174 Angle : 0.484 5.858 11120 Z= 0.264 Chirality : 0.040 0.148 1271 Planarity : 0.004 0.049 1410 Dihedral : 6.341 88.491 1159 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.27 % Allowed : 13.52 % Favored : 84.20 % 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: 1.59 (0.27), residues: 1001 helix: 2.29 (0.25), residues: 422 sheet: 0.11 (0.33), residues: 236 loop : 0.30 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE N 108 TYR 0.013 0.001 TYR A 339 ARG 0.008 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5140 (mm) REVERT: R 161 MET cc_start: 0.6529 (mmt) cc_final: 0.6242 (tpp) REVERT: R 281 MET cc_start: 0.8816 (mmt) cc_final: 0.7999 (mmt) REVERT: B 226 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 254 ASP cc_start: 0.7760 (p0) cc_final: 0.7339 (t0) REVERT: G 47 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7215 (mt-10) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.2112 time to fit residues: 44.0305 Evaluate side-chains 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 73 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 0.0010 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 overall best weight: 0.7526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8213 Z= 0.154 Angle : 0.471 5.466 11120 Z= 0.257 Chirality : 0.040 0.140 1271 Planarity : 0.004 0.048 1410 Dihedral : 6.231 85.069 1159 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % Favored : 84.09 % 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: 1.66 (0.27), residues: 1001 helix: 2.41 (0.25), residues: 420 sheet: 0.08 (0.33), residues: 239 loop : 0.32 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR A 339 ARG 0.007 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5881 (tt) cc_final: 0.5075 (mm) REVERT: R 161 MET cc_start: 0.6485 (mmt) cc_final: 0.6199 (tpp) REVERT: R 281 MET cc_start: 0.8759 (mmt) cc_final: 0.7861 (mmt) REVERT: B 226 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7424 (mt-10) REVERT: B 254 ASP cc_start: 0.7745 (p0) cc_final: 0.7347 (t0) REVERT: G 17 GLU cc_start: 0.8183 (pm20) cc_final: 0.7977 (pm20) REVERT: G 47 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7199 (mt-10) outliers start: 20 outliers final: 19 residues processed: 160 average time/residue: 0.2148 time to fit residues: 45.7677 Evaluate side-chains 162 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4305 > 50: distance: 27 - 143: 28.289 distance: 30 - 140: 23.712 distance: 39 - 123: 24.471 distance: 42 - 120: 10.551 distance: 79 - 81: 11.271 distance: 81 - 82: 22.182 distance: 82 - 83: 30.285 distance: 82 - 85: 14.766 distance: 83 - 84: 23.788 distance: 83 - 89: 10.456 distance: 85 - 86: 19.947 distance: 86 - 88: 6.060 distance: 89 - 90: 4.546 distance: 90 - 91: 10.977 distance: 90 - 93: 6.218 distance: 91 - 92: 14.664 distance: 91 - 96: 13.077 distance: 93 - 95: 14.653 distance: 96 - 97: 9.625 distance: 97 - 98: 14.400 distance: 97 - 100: 27.648 distance: 98 - 99: 16.409 distance: 98 - 107: 5.210 distance: 100 - 101: 28.607 distance: 101 - 102: 6.485 distance: 102 - 103: 11.100 distance: 103 - 104: 3.471 distance: 104 - 105: 16.842 distance: 107 - 108: 9.632 distance: 108 - 109: 4.384 distance: 108 - 111: 10.253 distance: 109 - 110: 6.267 distance: 109 - 114: 11.835 distance: 111 - 112: 11.571 distance: 111 - 113: 24.452 distance: 114 - 115: 10.724 distance: 115 - 116: 6.938 distance: 115 - 118: 10.031 distance: 116 - 117: 13.620 distance: 116 - 120: 6.294 distance: 118 - 119: 19.943 distance: 120 - 121: 11.945 distance: 121 - 122: 12.769 distance: 121 - 124: 11.853 distance: 122 - 123: 17.735 distance: 122 - 131: 15.093 distance: 124 - 125: 15.046 distance: 125 - 126: 13.113 distance: 126 - 127: 14.974 distance: 127 - 128: 7.926 distance: 128 - 129: 13.584 distance: 128 - 130: 9.147 distance: 131 - 132: 13.046 distance: 132 - 133: 15.282 distance: 132 - 135: 16.028 distance: 133 - 134: 10.334 distance: 133 - 140: 9.672 distance: 137 - 139: 3.568 distance: 140 - 141: 3.271 distance: 141 - 142: 10.644 distance: 141 - 144: 12.787 distance: 142 - 143: 17.387 distance: 142 - 148: 19.428 distance: 144 - 145: 17.578 distance: 145 - 146: 14.215 distance: 145 - 147: 12.074 distance: 148 - 149: 21.970 distance: 149 - 150: 39.935 distance: 149 - 152: 42.483 distance: 150 - 151: 5.165 distance: 150 - 153: 12.047 distance: 153 - 154: 22.082 distance: 154 - 155: 5.218 distance: 155 - 156: 26.389 distance: 155 - 157: 11.696