Starting phenix.real_space_refine on Fri Jul 19 14:03:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/07_2024/8w87_37347_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/07_2024/8w87_37347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/07_2024/8w87_37347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/07_2024/8w87_37347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/07_2024/8w87_37347_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/07_2024/8w87_37347_neut.cif" } resolution = 2.8 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5235 2.51 5 N 1415 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 224": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "R ASP 21": "OD1" <-> "OD2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1906 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2315 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'B40': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.62 Number of scatterers: 8228 At special positions: 0 Unit cell: (82.4, 98.88, 132.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1515 8.00 N 1415 7.00 C 5235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.26 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 R 501 " Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 33 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.934A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.511A pdb=" N PHE A 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 253 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.749A pdb=" N ILE A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 365 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.524A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.812A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 87 Processing helix chain 'R' and resid 91 through 127 removed outlier: 4.282A pdb=" N PHE R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 231 removed outlier: 3.990A pdb=" N LEU R 231 " --> pdb=" O ALA R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 278 removed outlier: 3.610A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 305 removed outlier: 3.631A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 198 removed outlier: 4.685A pdb=" N VAL A 208 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLY A 47 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 227 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 228 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE A 264 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 230 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN A 266 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 232 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.944A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.358A 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: 6.743A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.239A 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 151 removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.839A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A 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: 6.695A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.840A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.851A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1386 1.32 - 1.44: 2303 1.44 - 1.57: 4625 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8406 Sorted by residual: bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.334 1.415 -0.082 1.23e-02 6.61e+03 4.39e+01 bond pdb=" C ASP R 103 " pdb=" N ILE R 104 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.25e-02 6.40e+03 3.74e+01 bond pdb=" C ASP R 103 " pdb=" O ASP R 103 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.15e-02 7.56e+03 9.89e+00 bond pdb=" CB ASP R 103 " pdb=" CG ASP R 103 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.57e-02 4.06e+03 3.05e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.21: 222 107.21 - 113.94: 4701 113.94 - 120.67: 3468 120.67 - 127.39: 2904 127.39 - 134.12: 89 Bond angle restraints: 11384 Sorted by residual: angle pdb=" C ASP R 103 " pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 110.96 105.05 5.91 1.54e+00 4.22e-01 1.47e+01 angle pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sigma weight residual 115.05 104.23 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" C B40 R 501 " ideal model delta sigma weight residual 114.49 104.29 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 108.63 3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 112.56 -3.96 1.46e+00 4.69e-01 7.37e+00 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.64: 4508 19.64 - 39.29: 381 39.29 - 58.93: 79 58.93 - 78.58: 16 78.58 - 98.22: 6 Dihedral angle restraints: 4990 sinusoidal: 1945 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB B40 R 501 " pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sinusoidal sigma weight residual 168.08 -93.70 -98.22 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1106 0.056 - 0.113: 144 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" C B40 R 501 " pdb=" CB B40 R 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.71 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP R 103 " pdb=" N ASP R 103 " pdb=" C ASP R 103 " pdb=" CB ASP R 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1272 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 284 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR R 284 " -0.059 2.00e-02 2.50e+03 pdb=" O THR R 284 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU R 285 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 282 " 0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO R 283 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.182 9.50e-02 1.11e+02 8.20e-02 4.90e+00 pdb=" NE ARG B 19 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.002 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 594 2.73 - 3.28: 8380 3.28 - 3.82: 13939 3.82 - 4.36: 17219 4.36 - 4.90: 30105 Nonbonded interactions: 70237 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.193 2.440 nonbonded pdb=" O ASN A 188 " pdb=" OG SER A 189 " model vdw 2.226 2.440 nonbonded pdb=" C B40 R 501 " pdb=" CM B40 R 501 " model vdw 2.251 3.104 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.314 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.319 2.440 ... (remaining 70232 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.430 Find NCS groups from input model: 0.100 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:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.003 0.082 8406 Z= 0.217 Angle : 0.561 10.817 11384 Z= 0.318 Chirality : 0.041 0.282 1275 Planarity : 0.005 0.083 1448 Dihedral : 15.674 98.222 3019 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.45 % Allowed : 16.10 % Favored : 83.45 % 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: 1.49 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 416 sheet: 0.46 (0.34), residues: 228 loop : -0.01 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 291 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 70 TYR 0.008 0.001 TYR A 313 ARG 0.015 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7653 (mtm110) REVERT: B 17 GLN cc_start: 0.6251 (tt0) cc_final: 0.6005 (tm130) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 1.3408 time to fit residues: 184.7199 Evaluate side-chains 124 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8406 Z= 0.194 Angle : 0.520 6.661 11384 Z= 0.283 Chirality : 0.042 0.163 1275 Planarity : 0.004 0.065 1448 Dihedral : 5.600 59.307 1149 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.91 % Allowed : 15.43 % Favored : 82.66 % 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: 1.58 (0.27), residues: 1031 helix: 2.27 (0.25), residues: 421 sheet: 0.49 (0.36), residues: 214 loop : 0.11 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS G 44 PHE 0.020 0.002 PHE R 165 TYR 0.026 0.001 TYR R 27 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.897 Fit side-chains REVERT: A 200 LYS cc_start: 0.8909 (mttp) cc_final: 0.8605 (mmtt) REVERT: A 213 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7968 (p0) REVERT: A 321 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7029 (mtp85) REVERT: A 355 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8251 (t0) REVERT: R 80 SER cc_start: 0.8109 (t) cc_final: 0.7239 (p) outliers start: 17 outliers final: 7 residues processed: 140 average time/residue: 1.3171 time to fit residues: 195.2674 Evaluate side-chains 136 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8406 Z= 0.306 Angle : 0.549 7.518 11384 Z= 0.297 Chirality : 0.044 0.158 1275 Planarity : 0.004 0.058 1448 Dihedral : 5.376 57.094 1148 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.38 % Allowed : 15.20 % Favored : 81.42 % 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: 1.40 (0.26), residues: 1031 helix: 2.09 (0.25), residues: 420 sheet: 0.41 (0.34), residues: 228 loop : 0.03 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 218 HIS 0.005 0.001 HIS G 44 PHE 0.016 0.002 PHE B 292 TYR 0.011 0.001 TYR R 27 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.002 Fit side-chains REVERT: A 58 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7958 (mptt) REVERT: A 200 LYS cc_start: 0.8947 (mttp) cc_final: 0.8620 (mmtm) REVERT: A 213 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 321 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7092 (mtp85) REVERT: A 355 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8268 (t0) REVERT: B 251 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8629 (mtt-85) REVERT: N 108 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: R 80 SER cc_start: 0.8057 (t) cc_final: 0.7155 (p) outliers start: 30 outliers final: 14 residues processed: 152 average time/residue: 1.2299 time to fit residues: 198.3392 Evaluate side-chains 145 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 0.0470 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8406 Z= 0.145 Angle : 0.471 5.908 11384 Z= 0.255 Chirality : 0.040 0.148 1275 Planarity : 0.004 0.055 1448 Dihedral : 5.080 59.978 1148 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 17.23 % Favored : 80.07 % 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: 1.57 (0.27), residues: 1031 helix: 2.27 (0.25), residues: 421 sheet: 0.44 (0.35), residues: 221 loop : 0.12 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.002 0.001 HIS G 44 PHE 0.014 0.001 PHE R 165 TYR 0.015 0.001 TYR R 27 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.959 Fit side-chains REVERT: A 58 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8000 (mptt) REVERT: A 200 LYS cc_start: 0.8925 (mttp) cc_final: 0.8624 (mmtm) REVERT: A 321 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7065 (mtp85) REVERT: A 355 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8285 (t0) REVERT: B 175 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: B 237 ASN cc_start: 0.8059 (t0) cc_final: 0.7808 (t0) REVERT: R 135 MET cc_start: 0.8850 (mmp) cc_final: 0.8488 (mmt) outliers start: 24 outliers final: 10 residues processed: 154 average time/residue: 1.1700 time to fit residues: 191.5758 Evaluate side-chains 141 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 239 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8406 Z= 0.163 Angle : 0.470 5.687 11384 Z= 0.254 Chirality : 0.041 0.147 1275 Planarity : 0.004 0.055 1448 Dihedral : 4.925 57.551 1148 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.27 % Allowed : 17.12 % Favored : 79.62 % 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: 1.60 (0.27), residues: 1031 helix: 2.30 (0.25), residues: 421 sheet: 0.41 (0.35), residues: 223 loop : 0.16 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 196 TYR 0.008 0.001 TYR N 95 ARG 0.009 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7675 (tmtt) REVERT: A 200 LYS cc_start: 0.8923 (mttp) cc_final: 0.8632 (mmtm) REVERT: A 213 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7731 (p0) REVERT: A 321 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7064 (mtp85) REVERT: A 355 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8244 (t0) outliers start: 29 outliers final: 15 residues processed: 152 average time/residue: 1.3248 time to fit residues: 213.6350 Evaluate side-chains 146 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8406 Z= 0.221 Angle : 0.496 6.057 11384 Z= 0.269 Chirality : 0.042 0.168 1275 Planarity : 0.004 0.053 1448 Dihedral : 4.986 57.583 1148 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.49 % Allowed : 17.57 % Favored : 78.94 % 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: 1.52 (0.27), residues: 1031 helix: 2.30 (0.25), residues: 420 sheet: 0.39 (0.35), residues: 221 loop : 0.03 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS R 63 PHE 0.013 0.001 PHE A 196 TYR 0.014 0.001 TYR R 27 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7691 (tmtt) REVERT: A 200 LYS cc_start: 0.8935 (mttp) cc_final: 0.8633 (mmtm) REVERT: A 213 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7714 (p0) REVERT: A 321 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7086 (mtp85) REVERT: A 355 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8266 (t0) REVERT: N 123 GLN cc_start: 0.8812 (tp40) cc_final: 0.8578 (mm-40) outliers start: 31 outliers final: 19 residues processed: 156 average time/residue: 1.1757 time to fit residues: 195.4773 Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8406 Z= 0.161 Angle : 0.469 5.577 11384 Z= 0.254 Chirality : 0.041 0.163 1275 Planarity : 0.004 0.054 1448 Dihedral : 4.792 57.686 1148 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.83 % Allowed : 17.45 % Favored : 78.72 % 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: 1.60 (0.27), residues: 1031 helix: 2.35 (0.25), residues: 421 sheet: 0.38 (0.35), residues: 223 loop : 0.12 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 291 HIS 0.002 0.001 HIS G 44 PHE 0.012 0.001 PHE A 196 TYR 0.010 0.001 TYR R 279 ARG 0.012 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7667 (tmtt) REVERT: A 200 LYS cc_start: 0.8926 (mttp) cc_final: 0.8639 (mmtt) REVERT: A 213 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 321 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7052 (mtp85) REVERT: A 355 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8279 (t0) REVERT: B 175 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: B 237 ASN cc_start: 0.8036 (t0) cc_final: 0.7801 (t0) REVERT: B 259 GLN cc_start: 0.7563 (tt0) cc_final: 0.6990 (mt0) REVERT: N 123 GLN cc_start: 0.8803 (tp40) cc_final: 0.8537 (mm-40) outliers start: 34 outliers final: 17 residues processed: 163 average time/residue: 1.1256 time to fit residues: 195.3877 Evaluate side-chains 155 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8406 Z= 0.216 Angle : 0.508 6.932 11384 Z= 0.272 Chirality : 0.042 0.163 1275 Planarity : 0.004 0.064 1448 Dihedral : 4.877 57.904 1148 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.83 % Allowed : 17.57 % Favored : 78.60 % 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 (0.26), residues: 1031 helix: 2.33 (0.25), residues: 420 sheet: 0.43 (0.34), residues: 219 loop : -0.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS R 63 PHE 0.013 0.001 PHE A 196 TYR 0.014 0.001 TYR R 27 ARG 0.018 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7686 (tmtt) REVERT: A 200 LYS cc_start: 0.8931 (mttp) cc_final: 0.8623 (mmtm) REVERT: A 213 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7658 (p0) REVERT: A 321 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7085 (mtp85) REVERT: A 355 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8254 (t0) REVERT: B 175 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: B 186 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: B 214 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7985 (tpp80) REVERT: B 259 GLN cc_start: 0.7527 (tt0) cc_final: 0.6888 (mt0) REVERT: R 23 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5625 (ptt90) outliers start: 34 outliers final: 22 residues processed: 157 average time/residue: 1.1537 time to fit residues: 192.6920 Evaluate side-chains 158 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8406 Z= 0.171 Angle : 0.493 6.975 11384 Z= 0.264 Chirality : 0.041 0.190 1275 Planarity : 0.004 0.081 1448 Dihedral : 4.702 57.334 1148 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.60 % Allowed : 18.13 % Favored : 78.27 % 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: 1031 helix: 2.34 (0.25), residues: 421 sheet: 0.42 (0.35), residues: 221 loop : 0.09 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 291 HIS 0.002 0.001 HIS R 63 PHE 0.013 0.001 PHE R 154 TYR 0.010 0.001 TYR R 123 ARG 0.019 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7691 (tmtt) REVERT: A 200 LYS cc_start: 0.8927 (mttp) cc_final: 0.8633 (mmtt) REVERT: A 213 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7657 (p0) REVERT: A 321 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7075 (mtp85) REVERT: A 355 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8247 (t0) REVERT: B 175 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: B 186 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: B 237 ASN cc_start: 0.8053 (t0) cc_final: 0.7835 (t0) REVERT: B 259 GLN cc_start: 0.7471 (tt0) cc_final: 0.6992 (mt0) REVERT: N 123 GLN cc_start: 0.8730 (tp40) cc_final: 0.8463 (mm-40) REVERT: R 23 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.5539 (ptm-80) outliers start: 32 outliers final: 20 residues processed: 153 average time/residue: 1.1978 time to fit residues: 194.9170 Evaluate side-chains 159 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.0010 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8406 Z= 0.160 Angle : 0.488 7.406 11384 Z= 0.261 Chirality : 0.041 0.149 1275 Planarity : 0.004 0.080 1448 Dihedral : 4.458 57.117 1146 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.04 % Allowed : 18.81 % Favored : 78.15 % 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: 1.60 (0.27), residues: 1031 helix: 2.36 (0.25), residues: 421 sheet: 0.38 (0.35), residues: 223 loop : 0.11 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 291 HIS 0.002 0.001 HIS A 331 PHE 0.013 0.001 PHE R 154 TYR 0.011 0.001 TYR R 27 ARG 0.020 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7730 (tmtt) REVERT: A 200 LYS cc_start: 0.8918 (mttp) cc_final: 0.8631 (mmtt) REVERT: A 213 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7626 (p0) REVERT: A 321 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7112 (mtp85) REVERT: A 355 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8266 (t0) REVERT: B 175 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: B 186 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: B 237 ASN cc_start: 0.8059 (t0) cc_final: 0.7857 (t0) REVERT: B 259 GLN cc_start: 0.7361 (tt0) cc_final: 0.6969 (mt0) REVERT: N 80 TYR cc_start: 0.8410 (m-80) cc_final: 0.8038 (m-80) REVERT: N 123 GLN cc_start: 0.8706 (tp40) cc_final: 0.8439 (mm-40) REVERT: R 23 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.5542 (ptm-80) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 1.1601 time to fit residues: 187.3809 Evaluate side-chains 157 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107807 restraints weight = 9311.424| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.30 r_work: 0.3149 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 8406 Z= 0.150 Angle : 0.481 6.239 11384 Z= 0.258 Chirality : 0.040 0.143 1275 Planarity : 0.004 0.059 1448 Dihedral : 4.387 56.975 1146 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.59 % Allowed : 19.59 % Favored : 77.82 % 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: 1.66 (0.27), residues: 1031 helix: 2.41 (0.25), residues: 421 sheet: 0.48 (0.35), residues: 219 loop : 0.08 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 291 HIS 0.002 0.001 HIS G 44 PHE 0.014 0.001 PHE R 70 TYR 0.017 0.001 TYR N 60 ARG 0.014 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.38 seconds wall clock time: 64 minutes 20.28 seconds (3860.28 seconds total)