Starting phenix.real_space_refine on Sat Jul 20 16:21:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxg_40851/07_2024/8sxg_40851.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxg_40851/07_2024/8sxg_40851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxg_40851/07_2024/8sxg_40851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxg_40851/07_2024/8sxg_40851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxg_40851/07_2024/8sxg_40851.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxg_40851/07_2024/8sxg_40851.cif" } resolution = 4.14 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= 0.047 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 17 5.16 5 C 7109 2.51 5 N 2021 2.21 5 O 2225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11372 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2748 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2723 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 20, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4248 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 512} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1623 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 205} Chain breaks: 2 Time building chain proxies: 6.64, per 1000 atoms: 0.58 Number of scatterers: 11372 At special positions: 0 Unit cell: (91.908, 141.588, 142.83, 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 17 16.00 O 2225 8.00 N 2021 7.00 C 7109 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: 4.63 Conformation dependent library (CDL) restraints added in 2.1 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 55.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.902A pdb=" N LEU A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 82 removed outlier: 4.183A pdb=" N ASP A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.808A pdb=" N PHE A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.885A pdb=" N SER A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 removed outlier: 3.581A pdb=" N SER A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.873A pdb=" N LEU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.851A pdb=" N GLU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.631A pdb=" N GLU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.572A pdb=" N ALA B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.013A pdb=" N GLU B 276 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.637A pdb=" N GLN B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.791A pdb=" N SER B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 removed outlier: 4.022A pdb=" N VAL B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.617A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.741A pdb=" N ALA C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 154 through 163 removed outlier: 4.171A pdb=" N GLU C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.951A pdb=" N LEU C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 4.295A pdb=" N ALA C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 removed outlier: 4.075A pdb=" N ARG C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 233 removed outlier: 3.577A pdb=" N LEU C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 250 Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 253 through 267 removed outlier: 4.161A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.617A pdb=" N ARG C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 320 through 335 Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.958A pdb=" N VAL C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 369 removed outlier: 3.577A pdb=" N ALA C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 Processing helix chain 'C' and resid 385 through 403 removed outlier: 3.856A pdb=" N GLN C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 Processing helix chain 'C' and resid 423 through 438 removed outlier: 3.619A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 454 Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.678A pdb=" N LEU C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 492 through 507 Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.630A pdb=" N ALA C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'E' and resid 214 through 230 Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.682A pdb=" N PHE E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.866A pdb=" N SER E 416 " --> pdb=" O ARG E 412 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP E 417 " --> pdb=" O PRO E 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 412 through 417' Processing helix chain 'E' and resid 417 through 433 removed outlier: 3.558A pdb=" N SER E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.637A pdb=" N TYR A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 5.686A pdb=" N LYS A 343 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 334 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A 345 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 332 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.650A pdb=" N ALA A 187 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.996A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 138 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.996A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 138 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 171 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE A 143 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 169 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 200 removed outlier: 7.073A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 204 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP A 240 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 206 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 296 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114 removed outlier: 7.021A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 119 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 118 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 114 removed outlier: 7.021A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 119 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 118 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B 171 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 143 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR B 169 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 172 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 180 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.688A pdb=" N TYR B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 278 removed outlier: 3.646A pdb=" N LEU B 277 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 269 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 347 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AB4, first strand: chain 'E' and resid 197 through 200 removed outlier: 5.556A pdb=" N VAL E 198 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR E 205 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA E 204 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASP E 240 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU E 206 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU E 237 " --> pdb=" O VAL E 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 264 through 266 647 hydrogen bonds defined for protein. 1872 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: 3.53 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3954 1.34 - 1.46: 1228 1.46 - 1.57: 6320 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 11535 Sorted by residual: bond pdb=" CG GLU C 344 " pdb=" CD GLU C 344 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N SER B 193 " pdb=" CA SER B 193 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 6.02e-01 bond pdb=" C GLU A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.332 1.340 -0.008 1.12e-02 7.97e+03 5.73e-01 bond pdb=" N VAL B 290 " pdb=" CA VAL B 290 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.69e-01 bond pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.92e-01 ... (remaining 11530 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 332 107.23 - 113.92: 6458 113.92 - 120.61: 4749 120.61 - 127.30: 3974 127.30 - 133.99: 91 Bond angle restraints: 15604 Sorted by residual: angle pdb=" N ARG E 434 " pdb=" CA ARG E 434 " pdb=" CB ARG E 434 " ideal model delta sigma weight residual 114.17 110.82 3.35 1.14e+00 7.69e-01 8.65e+00 angle pdb=" N GLU C 344 " pdb=" CA GLU C 344 " pdb=" CB GLU C 344 " ideal model delta sigma weight residual 110.22 114.27 -4.05 1.54e+00 4.22e-01 6.92e+00 angle pdb=" C ALA B 302 " pdb=" CA ALA B 302 " pdb=" CB ALA B 302 " ideal model delta sigma weight residual 110.42 115.65 -5.23 1.99e+00 2.53e-01 6.91e+00 angle pdb=" C SER B 193 " pdb=" CA SER B 193 " pdb=" CB SER B 193 " ideal model delta sigma weight residual 110.42 115.60 -5.18 1.99e+00 2.53e-01 6.78e+00 angle pdb=" C LEU B 311 " pdb=" N GLN B 312 " pdb=" CA GLN B 312 " ideal model delta sigma weight residual 121.64 116.29 5.35 2.13e+00 2.20e-01 6.30e+00 ... (remaining 15599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6422 17.94 - 35.88: 568 35.88 - 53.82: 90 53.82 - 71.76: 13 71.76 - 89.70: 13 Dihedral angle restraints: 7106 sinusoidal: 2862 harmonic: 4244 Sorted by residual: dihedral pdb=" CA ASP A 313 " pdb=" C ASP A 313 " pdb=" N GLN A 314 " pdb=" CA GLN A 314 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN E 230 " pdb=" C ASN E 230 " pdb=" N LYS E 231 " pdb=" CA LYS E 231 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ALA A 58 " pdb=" C ALA A 58 " pdb=" N ALA A 59 " pdb=" CA ALA A 59 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 7103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1175 0.028 - 0.056: 380 0.056 - 0.084: 104 0.084 - 0.112: 78 0.112 - 0.140: 34 Chirality restraints: 1771 Sorted by residual: chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 168 " pdb=" N ILE B 168 " pdb=" C ILE B 168 " pdb=" CB ILE B 168 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 143 " pdb=" N ILE A 143 " pdb=" C ILE A 143 " pdb=" CB ILE A 143 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1768 not shown) Planarity restraints: 2081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 89 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 90 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 415 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C GLU C 415 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU C 415 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY C 416 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 57 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LEU C 57 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU C 57 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 58 " -0.008 2.00e-02 2.50e+03 ... (remaining 2078 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 110 2.49 - 3.09: 9088 3.09 - 3.70: 18427 3.70 - 4.30: 25336 4.30 - 4.90: 41450 Nonbonded interactions: 94411 Sorted by model distance: nonbonded pdb=" OG SER B 193 " pdb=" OE1 GLU B 218 " model vdw 1.889 2.440 nonbonded pdb=" O ASN E 297 " pdb=" OG1 THR E 322 " model vdw 2.038 2.440 nonbonded pdb=" O SER B 193 " pdb=" OG1 THR B 209 " model vdw 2.063 2.440 nonbonded pdb=" NH1 ARG B 207 " pdb=" O ILE B 208 " model vdw 2.073 2.520 nonbonded pdb=" O VAL E 248 " pdb=" OG SER E 251 " model vdw 2.091 2.440 ... (remaining 94406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 373 or resid 410 through 436)) selection = chain 'B' } 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 group one per residue 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: 1.650 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.002 0.026 11535 Z= 0.147 Angle : 0.499 5.347 15604 Z= 0.263 Chirality : 0.038 0.140 1771 Planarity : 0.004 0.050 2081 Dihedral : 14.007 89.698 4378 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1461 helix: 1.78 (0.20), residues: 745 sheet: -0.96 (0.42), residues: 178 loop : -0.72 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 537 HIS 0.006 0.001 HIS C 325 PHE 0.010 0.001 PHE C 326 TYR 0.012 0.001 TYR C 54 ARG 0.003 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 MET cc_start: 0.1539 (tpp) cc_final: 0.1306 (tpp) REVERT: E 265 ILE cc_start: 0.8830 (mm) cc_final: 0.8468 (mm) REVERT: E 320 MET cc_start: 0.8992 (ttp) cc_final: 0.8589 (ttt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2913 time to fit residues: 27.6238 Evaluate side-chains 44 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 59 optimal weight: 0.0970 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.0070 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11535 Z= 0.159 Angle : 0.531 6.691 15604 Z= 0.272 Chirality : 0.040 0.142 1771 Planarity : 0.004 0.033 2081 Dihedral : 4.091 18.092 1613 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 1.02 (0.23), residues: 1461 helix: 1.88 (0.19), residues: 772 sheet: -0.56 (0.44), residues: 159 loop : -0.71 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 537 HIS 0.004 0.001 HIS C 218 PHE 0.009 0.001 PHE B 104 TYR 0.016 0.001 TYR C 54 ARG 0.005 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8373 (p) cc_final: 0.8084 (t) REVERT: C 432 MET cc_start: 0.1427 (tpp) cc_final: 0.1160 (tpp) REVERT: C 575 PRO cc_start: 0.1852 (Cg_endo) cc_final: 0.1371 (Cg_exo) REVERT: E 265 ILE cc_start: 0.8817 (mm) cc_final: 0.8366 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2707 time to fit residues: 22.9266 Evaluate side-chains 44 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 118 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN C 147 ASN C 518 GLN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11535 Z= 0.254 Angle : 0.568 6.283 15604 Z= 0.289 Chirality : 0.040 0.145 1771 Planarity : 0.004 0.048 2081 Dihedral : 4.383 20.206 1613 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1461 helix: 1.73 (0.19), residues: 773 sheet: -0.66 (0.43), residues: 165 loop : -0.63 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 410 HIS 0.002 0.001 HIS C 218 PHE 0.011 0.001 PHE B 211 TYR 0.020 0.002 TYR B 205 ARG 0.006 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 MET cc_start: 0.1457 (tpp) cc_final: 0.1185 (tpp) REVERT: C 575 PRO cc_start: 0.2278 (Cg_endo) cc_final: 0.1907 (Cg_exo) REVERT: E 265 ILE cc_start: 0.8915 (mm) cc_final: 0.8492 (mm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2956 time to fit residues: 20.7003 Evaluate side-chains 40 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN E 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11535 Z= 0.350 Angle : 0.640 7.632 15604 Z= 0.324 Chirality : 0.042 0.149 1771 Planarity : 0.005 0.039 2081 Dihedral : 4.806 22.862 1613 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1461 helix: 1.30 (0.18), residues: 777 sheet: -0.81 (0.43), residues: 163 loop : -0.69 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 537 HIS 0.004 0.001 HIS C 218 PHE 0.016 0.002 PHE B 211 TYR 0.023 0.002 TYR B 205 ARG 0.005 0.001 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8564 (p) cc_final: 0.8178 (t) REVERT: C 432 MET cc_start: 0.1589 (tpp) cc_final: 0.1363 (tpp) REVERT: C 575 PRO cc_start: 0.1740 (Cg_endo) cc_final: 0.1520 (Cg_exo) REVERT: E 265 ILE cc_start: 0.8952 (mm) cc_final: 0.8494 (mm) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.2670 time to fit residues: 20.1033 Evaluate side-chains 41 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 314 GLN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11535 Z= 0.224 Angle : 0.566 7.093 15604 Z= 0.285 Chirality : 0.040 0.151 1771 Planarity : 0.004 0.035 2081 Dihedral : 4.523 20.823 1613 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1461 helix: 1.45 (0.18), residues: 779 sheet: -0.79 (0.43), residues: 165 loop : -0.68 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 537 HIS 0.002 0.001 HIS C 218 PHE 0.019 0.001 PHE B 93 TYR 0.018 0.002 TYR B 205 ARG 0.004 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8498 (p) cc_final: 0.8193 (t) REVERT: C 432 MET cc_start: 0.1664 (tpp) cc_final: 0.1434 (tpp) REVERT: C 575 PRO cc_start: 0.2245 (Cg_endo) cc_final: 0.2007 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2633 time to fit residues: 20.9042 Evaluate side-chains 40 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11535 Z= 0.184 Angle : 0.545 7.594 15604 Z= 0.273 Chirality : 0.040 0.142 1771 Planarity : 0.004 0.036 2081 Dihedral : 4.333 18.892 1613 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1461 helix: 1.49 (0.18), residues: 778 sheet: -0.81 (0.42), residues: 175 loop : -0.68 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 537 HIS 0.001 0.000 HIS C 218 PHE 0.013 0.001 PHE B 93 TYR 0.014 0.001 TYR A 349 ARG 0.004 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8525 (p) cc_final: 0.8259 (t) REVERT: C 432 MET cc_start: 0.1624 (tpp) cc_final: 0.1219 (tpp) REVERT: C 575 PRO cc_start: 0.1813 (Cg_endo) cc_final: 0.1569 (Cg_exo) REVERT: E 265 ILE cc_start: 0.8910 (mm) cc_final: 0.8483 (mm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2324 time to fit residues: 17.9465 Evaluate side-chains 39 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11535 Z= 0.244 Angle : 0.574 7.602 15604 Z= 0.290 Chirality : 0.041 0.160 1771 Planarity : 0.004 0.036 2081 Dihedral : 4.412 19.837 1613 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1461 helix: 1.39 (0.18), residues: 781 sheet: -0.90 (0.41), residues: 175 loop : -0.66 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 537 HIS 0.003 0.001 HIS C 218 PHE 0.012 0.001 PHE B 211 TYR 0.021 0.002 TYR B 205 ARG 0.004 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8569 (p) cc_final: 0.8298 (t) REVERT: C 432 MET cc_start: 0.1374 (tpp) cc_final: 0.0972 (tpp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2385 time to fit residues: 17.3392 Evaluate side-chains 37 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 314 GLN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11535 Z= 0.221 Angle : 0.561 7.206 15604 Z= 0.281 Chirality : 0.040 0.137 1771 Planarity : 0.004 0.036 2081 Dihedral : 4.380 19.541 1613 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1461 helix: 1.39 (0.18), residues: 781 sheet: -0.90 (0.41), residues: 175 loop : -0.71 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 537 HIS 0.002 0.000 HIS C 218 PHE 0.009 0.001 PHE B 93 TYR 0.024 0.002 TYR B 203 ARG 0.003 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8543 (p) cc_final: 0.8258 (t) REVERT: C 432 MET cc_start: 0.1613 (tpp) cc_final: 0.1205 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2526 time to fit residues: 19.2605 Evaluate side-chains 37 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11535 Z= 0.180 Angle : 0.538 6.772 15604 Z= 0.269 Chirality : 0.040 0.136 1771 Planarity : 0.004 0.037 2081 Dihedral : 4.246 18.798 1613 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.60 (0.22), residues: 1461 helix: 1.47 (0.18), residues: 781 sheet: -0.89 (0.41), residues: 174 loop : -0.74 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 537 HIS 0.001 0.000 HIS C 218 PHE 0.009 0.001 PHE B 93 TYR 0.017 0.001 TYR B 203 ARG 0.003 0.000 ARG C 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8520 (p) cc_final: 0.8249 (t) REVERT: C 432 MET cc_start: 0.1617 (tpp) cc_final: 0.1184 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2581 time to fit residues: 18.4576 Evaluate side-chains 39 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.0370 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 12 optimal weight: 0.0370 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11535 Z= 0.153 Angle : 0.525 8.327 15604 Z= 0.261 Chirality : 0.039 0.137 1771 Planarity : 0.004 0.037 2081 Dihedral : 4.049 16.404 1613 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1461 helix: 1.61 (0.19), residues: 777 sheet: -0.82 (0.42), residues: 174 loop : -0.79 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 537 HIS 0.001 0.000 HIS C 531 PHE 0.009 0.001 PHE B 104 TYR 0.015 0.001 TYR C 54 ARG 0.007 0.000 ARG C 471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.8551 (p) cc_final: 0.8279 (t) REVERT: C 432 MET cc_start: 0.1586 (tpp) cc_final: 0.1176 (tpp) REVERT: C 440 LEU cc_start: 0.6953 (mt) cc_final: 0.6721 (tp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2481 time to fit residues: 18.9298 Evaluate side-chains 40 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 116 optimal weight: 20.0000 chunk 48 optimal weight: 0.0570 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.094653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.076192 restraints weight = 55541.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.074533 restraints weight = 55382.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075307 restraints weight = 53918.877| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11535 Z= 0.153 Angle : 0.516 6.775 15604 Z= 0.256 Chirality : 0.039 0.133 1771 Planarity : 0.004 0.037 2081 Dihedral : 3.971 16.359 1613 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1461 helix: 1.64 (0.19), residues: 778 sheet: -0.78 (0.42), residues: 175 loop : -0.83 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 537 HIS 0.001 0.000 HIS C 531 PHE 0.008 0.001 PHE B 104 TYR 0.014 0.001 TYR C 54 ARG 0.005 0.000 ARG C 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.96 seconds wall clock time: 36 minutes 1.13 seconds (2161.13 seconds total)