Starting phenix.real_space_refine on Wed Feb 14 20:13:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btx_30190/02_2024/7btx_30190.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btx_30190/02_2024/7btx_30190.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/7btx_30190/02_2024/7btx_30190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btx_30190/02_2024/7btx_30190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btx_30190/02_2024/7btx_30190.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btx_30190/02_2024/7btx_30190.pdb" } 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= 0.000 sd= 0.008 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 44 5.16 5 C 6512 2.51 5 N 1724 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 148": "OD1" <-> "OD2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ASP 293": "OD1" <-> "OD2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 160": "NH1" <-> "NH2" Residue "L ARG 192": "NH1" <-> "NH2" Residue "L ARG 209": "NH1" <-> "NH2" Residue "L TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 263": "NH1" <-> "NH2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2399 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2439 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2555 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.93, per 1000 atoms: 0.58 Number of scatterers: 10168 At special positions: 0 Unit cell: (106.24, 101.26, 101.26, 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 44 16.00 O 1888 8.00 N 1724 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 33.8% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.601A pdb=" N LYS A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.503A pdb=" N LYS A 356 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.872A pdb=" N ILE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.546A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.677A pdb=" N ARG B 153 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 181 removed outlier: 3.539A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.571A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.637A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 242 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.658A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.581A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.543A pdb=" N PHE B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.770A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.813A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 204 through 241 removed outlier: 3.754A pdb=" N ASN C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 210 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.572A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 removed outlier: 4.244A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.708A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.853A pdb=" N SER C 318 " --> pdb=" O VAL C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.865A pdb=" N TYR C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 19 through 23 removed outlier: 3.609A pdb=" N ASN L 22 " --> pdb=" O SER L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.829A pdb=" N LYS L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 7.544A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 296 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 removed outlier: 7.544A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 296 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 21 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.196A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 194 through 199 removed outlier: 3.538A pdb=" N LEU L 179 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR L 165 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N TYR L 491 " --> pdb=" O HIS L 44 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN L 46 " --> pdb=" O TYR L 491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 209 through 211 removed outlier: 3.540A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 209 through 211 removed outlier: 3.540A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU L 269 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG L 263 " --> pdb=" O SER L 258 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN L 306 " --> pdb=" O ASP L 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 313 through 316 649 hydrogen bonds defined for protein. 1848 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: 3.57 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1632 1.28 - 1.41: 2707 1.41 - 1.55: 5952 1.55 - 1.68: 30 1.68 - 1.82: 65 Bond restraints: 10386 Sorted by residual: bond pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 1.523 1.423 0.100 1.34e-02 5.57e+03 5.57e+01 bond pdb=" C ASP A 134 " pdb=" O ASP A 134 " ideal model delta sigma weight residual 1.235 1.154 0.081 1.14e-02 7.69e+03 5.07e+01 bond pdb=" C ASN A 135 " pdb=" O ASN A 135 " ideal model delta sigma weight residual 1.235 1.168 0.068 1.26e-02 6.30e+03 2.88e+01 bond pdb=" CG ASN A 135 " pdb=" ND2 ASN A 135 " ideal model delta sigma weight residual 1.328 1.218 0.110 2.10e-02 2.27e+03 2.72e+01 bond pdb=" N ASN A 135 " pdb=" CA ASN A 135 " ideal model delta sigma weight residual 1.457 1.395 0.063 1.29e-02 6.01e+03 2.37e+01 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.90: 161 105.90 - 113.35: 5684 113.35 - 120.80: 4735 120.80 - 128.25: 3361 128.25 - 135.70: 93 Bond angle restraints: 14034 Sorted by residual: angle pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" C GLU C 98 " ideal model delta sigma weight residual 109.06 129.71 -20.65 1.70e+00 3.46e-01 1.48e+02 angle pdb=" C LEU A 152 " pdb=" N LYS A 153 " pdb=" CA LYS A 153 " ideal model delta sigma weight residual 121.54 135.70 -14.16 1.91e+00 2.74e-01 5.49e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 122.95 132.10 -9.15 1.44e+00 4.82e-01 4.04e+01 angle pdb=" N THR C 87 " pdb=" CA THR C 87 " pdb=" C THR C 87 " ideal model delta sigma weight residual 110.80 123.76 -12.96 2.13e+00 2.20e-01 3.70e+01 angle pdb=" C TYR C 150 " pdb=" N PHE C 151 " pdb=" CA PHE C 151 " ideal model delta sigma weight residual 120.58 128.56 -7.98 1.32e+00 5.74e-01 3.65e+01 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5514 17.47 - 34.95: 534 34.95 - 52.42: 106 52.42 - 69.89: 19 69.89 - 87.37: 13 Dihedral angle restraints: 6186 sinusoidal: 2480 harmonic: 3706 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 123.89 56.11 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 129.92 50.08 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA TYR L 148 " pdb=" C TYR L 148 " pdb=" N PRO L 149 " pdb=" CA PRO L 149 " ideal model delta harmonic sigma weight residual 180.00 133.14 46.86 0 5.00e+00 4.00e-02 8.79e+01 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1555 0.166 - 0.331: 15 0.331 - 0.497: 0 0.497 - 0.663: 2 0.663 - 0.828: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA THR C 87 " pdb=" N THR C 87 " pdb=" C THR C 87 " pdb=" CB THR C 87 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA GLU C 98 " pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CB GLU C 98 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA PHE B 18 " pdb=" N PHE B 18 " pdb=" C PHE B 18 " pdb=" CB PHE B 18 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 1570 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 61 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 86 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C CYS C 86 " 0.077 2.00e-02 2.50e+03 pdb=" O CYS C 86 " -0.028 2.00e-02 2.50e+03 pdb=" N THR C 87 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " -0.071 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 129 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.061 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2791 2.80 - 3.33: 8218 3.33 - 3.85: 16487 3.85 - 4.38: 20074 4.38 - 4.90: 35542 Nonbonded interactions: 83112 Sorted by model distance: nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.280 2.440 nonbonded pdb=" OD1 ASP B 80 " pdb=" OH TYR B 192 " model vdw 2.297 2.440 nonbonded pdb=" O SER L 230 " pdb=" OG SER L 230 " model vdw 2.306 2.440 nonbonded pdb=" O SER L 302 " pdb=" OG SER L 302 " model vdw 2.315 2.440 nonbonded pdb=" O LEU C 109 " pdb=" OG SER C 113 " model vdw 2.317 2.440 ... (remaining 83107 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: 1.120 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: 4.680 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.690 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:21.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 0.110 10386 Z= 0.493 Angle : 1.094 20.654 14034 Z= 0.629 Chirality : 0.063 0.828 1573 Planarity : 0.008 0.114 1764 Dihedral : 14.926 87.369 3786 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.13 % Favored : 91.14 % Rotamer: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.66 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.57 % 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: -4.94 (0.18), residues: 1242 helix: -4.14 (0.12), residues: 389 sheet: -1.85 (0.24), residues: 397 loop : -3.55 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 323 HIS 0.014 0.002 HIS A 422 PHE 0.026 0.003 PHE B 68 TYR 0.018 0.002 TYR B 245 ARG 0.016 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.323 Fit side-chains REVERT: A 138 GLU cc_start: 0.7629 (tp30) cc_final: 0.7241 (mm-30) REVERT: A 169 HIS cc_start: 0.6932 (m90) cc_final: 0.6710 (m90) REVERT: B 248 HIS cc_start: 0.8311 (t70) cc_final: 0.8057 (t70) REVERT: B 255 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7454 (tt0) REVERT: C 267 ASP cc_start: 0.7849 (t70) cc_final: 0.7382 (t0) REVERT: L 315 GLN cc_start: 0.7116 (tp-100) cc_final: 0.6796 (tt0) REVERT: L 434 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7938 (tttm) outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 1.0748 time to fit residues: 205.7173 Evaluate side-chains 124 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 175 ASN A 187 ASN A 200 ASN A 207 GLN A 280 HIS A 318 ASN A 369 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 424 ASN A 466 HIS B 87 GLN B 94 ASN C 7 HIS C 67 ASN C 84 ASN C 136 ASN C 160 GLN C 208 ASN C 218 GLN C 222 ASN C 224 GLN C 277 GLN C 300 ASN C 301 ASN L 22 ASN L 57 ASN L 164 GLN L 180 ASN L 490 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10386 Z= 0.314 Angle : 0.720 8.595 14034 Z= 0.388 Chirality : 0.044 0.158 1573 Planarity : 0.007 0.095 1764 Dihedral : 7.227 49.406 1360 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.22 % Rotamer: Outliers : 2.82 % Allowed : 13.22 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % 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: -3.18 (0.21), residues: 1242 helix: -1.48 (0.21), residues: 402 sheet: -1.31 (0.26), residues: 386 loop : -3.29 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.006 0.001 HIS A 422 PHE 0.021 0.002 PHE A 237 TYR 0.015 0.002 TYR L 148 ARG 0.003 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.385 Fit side-chains REVERT: A 138 GLU cc_start: 0.7550 (tp30) cc_final: 0.7139 (mm-30) REVERT: B 196 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7403 (mtmt) REVERT: B 255 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7274 (tt0) REVERT: C 97 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.5213 (mt-10) REVERT: C 267 ASP cc_start: 0.7809 (t70) cc_final: 0.6975 (t0) REVERT: L 169 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (tt) REVERT: L 239 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8372 (tt) REVERT: L 315 GLN cc_start: 0.6665 (tp-100) cc_final: 0.6312 (tt0) REVERT: L 434 LYS cc_start: 0.7929 (ttpt) cc_final: 0.6944 (mptt) outliers start: 32 outliers final: 11 residues processed: 142 average time/residue: 0.9071 time to fit residues: 142.3144 Evaluate side-chains 121 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10386 Z= 0.195 Angle : 0.624 8.093 14034 Z= 0.335 Chirality : 0.041 0.136 1573 Planarity : 0.006 0.090 1764 Dihedral : 6.612 44.800 1360 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.05 % Favored : 91.71 % Rotamer: Outliers : 3.08 % Allowed : 14.80 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.23), residues: 1242 helix: 0.02 (0.26), residues: 404 sheet: -1.07 (0.26), residues: 394 loop : -3.08 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 169 PHE 0.022 0.001 PHE L 313 TYR 0.016 0.001 TYR L 185 ARG 0.003 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.288 Fit side-chains REVERT: A 138 GLU cc_start: 0.7561 (tp30) cc_final: 0.7198 (mm-30) REVERT: A 314 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: B 196 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7406 (mtmt) REVERT: B 255 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7291 (tt0) REVERT: C 267 ASP cc_start: 0.7766 (t70) cc_final: 0.6937 (t0) REVERT: C 302 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7749 (mp) REVERT: L 169 LEU cc_start: 0.8736 (mt) cc_final: 0.8523 (tt) REVERT: L 239 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8354 (tt) REVERT: L 315 GLN cc_start: 0.6665 (tp-100) cc_final: 0.6461 (mt0) REVERT: L 434 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7011 (mttt) outliers start: 35 outliers final: 11 residues processed: 146 average time/residue: 0.8605 time to fit residues: 139.2479 Evaluate side-chains 124 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10386 Z= 0.287 Angle : 0.658 7.864 14034 Z= 0.351 Chirality : 0.043 0.138 1573 Planarity : 0.006 0.092 1764 Dihedral : 6.584 47.551 1360 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 3.70 % Allowed : 16.12 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.76 (0.23), residues: 1242 helix: 0.57 (0.26), residues: 404 sheet: -0.97 (0.26), residues: 403 loop : -3.00 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.006 0.001 HIS A 169 PHE 0.018 0.002 PHE A 237 TYR 0.014 0.002 TYR L 296 ARG 0.005 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.201 Fit side-chains REVERT: A 138 GLU cc_start: 0.7559 (tp30) cc_final: 0.7168 (mm-30) REVERT: A 314 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: B 196 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7405 (mtmt) REVERT: B 255 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7249 (tt0) REVERT: C 226 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: C 267 ASP cc_start: 0.7787 (t70) cc_final: 0.6894 (t0) REVERT: L 169 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (tt) REVERT: L 239 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (tt) REVERT: L 434 LYS cc_start: 0.7880 (ttpt) cc_final: 0.6960 (mttt) outliers start: 42 outliers final: 26 residues processed: 141 average time/residue: 0.8794 time to fit residues: 137.5695 Evaluate side-chains 135 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10386 Z= 0.196 Angle : 0.606 7.630 14034 Z= 0.324 Chirality : 0.041 0.136 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.288 45.013 1360 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.73 % Favored : 92.03 % Rotamer: Outliers : 3.88 % Allowed : 16.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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 (0.24), residues: 1242 helix: 0.99 (0.27), residues: 406 sheet: -0.80 (0.26), residues: 400 loop : -2.90 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.003 0.001 HIS A 310 PHE 0.023 0.001 PHE L 313 TYR 0.013 0.001 TYR C 140 ARG 0.003 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 1.223 Fit side-chains REVERT: A 138 GLU cc_start: 0.7585 (tp30) cc_final: 0.7221 (mm-30) REVERT: A 213 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 314 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: B 255 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7297 (tt0) REVERT: C 267 ASP cc_start: 0.7713 (t70) cc_final: 0.6869 (t0) REVERT: C 302 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7868 (mp) REVERT: L 169 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8526 (tt) REVERT: L 434 LYS cc_start: 0.7885 (ttpt) cc_final: 0.6982 (mttp) outliers start: 44 outliers final: 19 residues processed: 145 average time/residue: 0.9080 time to fit residues: 145.0811 Evaluate side-chains 134 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN L 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10386 Z= 0.293 Angle : 0.659 7.666 14034 Z= 0.350 Chirality : 0.043 0.141 1573 Planarity : 0.005 0.090 1764 Dihedral : 6.374 47.177 1358 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 4.23 % Allowed : 16.21 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.31 (0.24), residues: 1242 helix: 1.14 (0.27), residues: 403 sheet: -0.79 (0.25), residues: 403 loop : -2.88 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 197 HIS 0.004 0.001 HIS A 422 PHE 0.017 0.002 PHE B 68 TYR 0.013 0.002 TYR B 164 ARG 0.005 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 1.259 Fit side-chains REVERT: A 138 GLU cc_start: 0.7565 (tp30) cc_final: 0.7190 (mm-30) REVERT: A 213 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8553 (m) REVERT: A 314 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: B 255 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7245 (tt0) REVERT: C 302 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7959 (mp) REVERT: L 7 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6752 (pt0) REVERT: L 169 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8506 (tt) REVERT: L 239 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8451 (tt) REVERT: L 434 LYS cc_start: 0.7876 (ttpt) cc_final: 0.6981 (mttp) outliers start: 48 outliers final: 27 residues processed: 143 average time/residue: 0.8767 time to fit residues: 138.7933 Evaluate side-chains 139 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10386 Z= 0.188 Angle : 0.603 7.400 14034 Z= 0.322 Chirality : 0.041 0.138 1573 Planarity : 0.005 0.086 1764 Dihedral : 6.110 44.386 1358 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.73 % Favored : 92.03 % Rotamer: Outliers : 4.05 % Allowed : 16.65 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.05 (0.24), residues: 1242 helix: 1.43 (0.27), residues: 409 sheet: -0.68 (0.26), residues: 402 loop : -2.85 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.003 0.001 HIS A 310 PHE 0.023 0.001 PHE L 313 TYR 0.034 0.001 TYR L 24 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.476 Fit side-chains REVERT: A 138 GLU cc_start: 0.7533 (tp30) cc_final: 0.7167 (mm-30) REVERT: A 213 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8551 (m) REVERT: A 314 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: B 255 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7291 (tt0) REVERT: C 111 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: C 302 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7885 (mp) REVERT: L 7 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: L 66 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7298 (ptp-110) REVERT: L 239 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8458 (tt) REVERT: L 434 LYS cc_start: 0.7883 (ttpt) cc_final: 0.6974 (mttp) outliers start: 46 outliers final: 20 residues processed: 148 average time/residue: 0.9939 time to fit residues: 161.4290 Evaluate side-chains 135 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 301 ASN L 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10386 Z= 0.168 Angle : 0.597 8.497 14034 Z= 0.314 Chirality : 0.040 0.137 1573 Planarity : 0.005 0.085 1764 Dihedral : 5.905 44.547 1358 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.89 % Favored : 91.87 % Rotamer: Outliers : 3.26 % Allowed : 18.06 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -0.82 (0.24), residues: 1242 helix: 1.72 (0.27), residues: 404 sheet: -0.58 (0.26), residues: 404 loop : -2.76 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.021 0.001 PHE L 313 TYR 0.027 0.001 TYR L 24 ARG 0.003 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.181 Fit side-chains REVERT: A 138 GLU cc_start: 0.7562 (tp30) cc_final: 0.7216 (pt0) REVERT: A 213 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8548 (m) REVERT: A 314 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: B 255 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7292 (tt0) REVERT: C 111 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: L 7 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6713 (pt0) REVERT: L 66 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7387 (ptp-110) REVERT: L 239 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8437 (tt) REVERT: L 434 LYS cc_start: 0.7869 (ttpt) cc_final: 0.6962 (mttp) outliers start: 37 outliers final: 16 residues processed: 139 average time/residue: 0.9320 time to fit residues: 143.0271 Evaluate side-chains 131 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN L 187 GLN L 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10386 Z= 0.260 Angle : 0.644 7.515 14034 Z= 0.339 Chirality : 0.042 0.136 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.100 46.877 1358 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.53 % Favored : 91.22 % Rotamer: Outliers : 2.82 % Allowed : 18.50 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1242 helix: 1.61 (0.27), residues: 399 sheet: -0.56 (0.26), residues: 401 loop : -2.77 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.003 0.001 HIS A 411 PHE 0.021 0.001 PHE L 313 TYR 0.027 0.002 TYR L 24 ARG 0.003 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.123 Fit side-chains REVERT: A 138 GLU cc_start: 0.7568 (tp30) cc_final: 0.7214 (mm-30) REVERT: A 213 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8565 (m) REVERT: A 314 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: B 139 ILE cc_start: 0.8719 (mp) cc_final: 0.8304 (mm) REVERT: B 255 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7264 (tt0) REVERT: C 111 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: L 7 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6769 (pt0) REVERT: L 66 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7449 (ptp-110) REVERT: L 239 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (tt) REVERT: L 434 LYS cc_start: 0.7876 (ttpt) cc_final: 0.6951 (mttp) outliers start: 32 outliers final: 19 residues processed: 133 average time/residue: 0.9178 time to fit residues: 134.6765 Evaluate side-chains 136 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN L 257 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10386 Z= 0.314 Angle : 0.681 7.713 14034 Z= 0.357 Chirality : 0.044 0.156 1573 Planarity : 0.005 0.087 1764 Dihedral : 6.281 47.438 1358 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.74 % Rotamer: Outliers : 2.73 % Allowed : 18.41 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % 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: -1.03 (0.24), residues: 1242 helix: 1.43 (0.27), residues: 404 sheet: -0.66 (0.26), residues: 402 loop : -2.78 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.004 0.001 HIS L 191 PHE 0.025 0.002 PHE L 313 TYR 0.029 0.002 TYR L 24 ARG 0.004 0.000 ARG A 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.257 Fit side-chains REVERT: A 138 GLU cc_start: 0.7570 (tp30) cc_final: 0.7196 (mm-30) REVERT: A 213 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8561 (m) REVERT: A 314 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: B 255 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7247 (tt0) REVERT: C 111 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: L 7 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6758 (pt0) REVERT: L 66 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7411 (ptp-110) REVERT: L 239 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8450 (tt) REVERT: L 434 LYS cc_start: 0.7876 (ttpt) cc_final: 0.6964 (mttt) outliers start: 31 outliers final: 21 residues processed: 135 average time/residue: 0.9484 time to fit residues: 140.8061 Evaluate side-chains 139 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 301 ASN L 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108350 restraints weight = 11792.380| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.07 r_work: 0.3047 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10386 Z= 0.194 Angle : 0.627 9.092 14034 Z= 0.329 Chirality : 0.041 0.137 1573 Planarity : 0.005 0.085 1764 Dihedral : 6.007 44.795 1358 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.89 % Favored : 91.87 % Rotamer: Outliers : 2.11 % Allowed : 19.30 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1242 helix: 1.75 (0.27), residues: 398 sheet: -0.58 (0.26), residues: 403 loop : -2.74 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.023 0.001 PHE L 313 TYR 0.024 0.001 TYR L 24 ARG 0.007 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.05 seconds wall clock time: 63 minutes 33.53 seconds (3813.53 seconds total)